Test procedures for predefined roles

This document defines a procedure for testing that the predefined roles can perform their work as intended. The main purpose is to weed out permission problems resulting from:

Incorrect permissions installed by installation program
Bugs in the permission handling in the core
Incorrect handling of permissions in the web client

The test procedure also tests that the basic functionality is working:

Creating items and linking them to other items
Defining import file formats
Importing array LIMS data
Importing and validating raw data against array LIMS data
Running analysis plug-ins
Using files instead of the database for storing data

Contents

Summary of the test procedure
Root user tests
Administrator tests
Power user tests
User tests
Analysis tests

Last updated: $Date: 2021-06-11 12:51:05 +0200 (Fri, 11 Jun 2021) $

1. Summary of the test procedure

Here is a summary of the test procedure:

Always start with a fresh installation.
The root user creates an administrator.
The administrator creates more users and some global resources:
- A group and three other users. One power user, one user and one guest.
- File formats for importing reporters
- Imports reporters
The power user creates item related to the project management:
- A project
- Protocols, one for each type of action: sampling, extraction, etc.
- Hardware and software that are used in the project
- Annotation types for annotations used in the project
- File formats for importing plates, print maps and raw data
- Array LIMS information - plate type, plates, array design, array batch and array slides
- Biomaterial LIMS information - bioplate type
The user creates items related to an actual experiment:
- Biomaterials: bioplate, biosources, samples, extracts, etc.
- Experiment: physical bioassays, derived bioassays, raw bioassays
- Import raw data
Both the user and the guest then do some analysis:
- Create a root bioassay set
- Filter the bioassay set
- Run a normalization plug-in
- Check the result by listing and plotting the data

These tests can also be run in automated mode by test programs. This will of course not test the web client, but are useful if one quickly needs to do parts of the test and then continue with, for example, the user or analysis tests on the web.

The data files needed by the tests are NOT included in the subversion repository. The main reason is that they are too large, and that we don't have permission to make them publicly available for download. To get the test file you need to be a core developer. Read the instructions on the DeveloperInformation page, Test data section on the BASE web site. The automated test programs require that file are placed (checked out) in the 'testdata' directory located in the BASE root directory. NOTE! Some test data files are bzip-compressed. Use the automatic unpacking that is built-in to BASE when uploading.

To run the tests do the following:

Compile the core and the test programs: ant main test.
Change to the build/test/ directory.
Run test programs: ./test.sh roles [OPTION] <cmds> where <cmds> is one or more of the following:
- all: run all tests
- root: run the root user tests
- admin: run the administrator tests
- power: run the power user tests
- user: run the regular user tests
- guest: run the guest user tests
and OPTION can be none or more of:
- -b: if the batch importers should be tested

2. Root user tests

The root user creates an administrator which is a server-wide admin.

Create a new user and set the following properties. All other properties may remain unchanged.

Name Login/Password Quota Quota group Membership

Admin admin/admin Unlimited - Roles: Administrator

Name	Login/Password	Quota	Quota group	Membership
Admin	admin/admin	Unlimited	-	Roles: Administrator

3. Administrator tests

The administrator creates users for a project and gives them permissions that are suitable for their role in the project. The administrator also sets up quota and group membership.

Create a new group and set the following properties:

Name Quota

Group A 1GB

Name	Quota
Group A	1GB

Create the following users:

Name	Login/Password	Quota	Quota group	Membership	Other
Power user	power/power	1GB	Group A	Roles: Power user	-
User	user/user	1GB	Group A	Roles: User	-
Guest	guest/guest	10MB	Group A	Roles: Guest	Multi-user account checked

Give USE permission for the listed users to the following plugins:

User	Plugins
Power user	Plate importer Reporter map importer Print map importer GTF reporter map importer Array design importer Array batch importer Array slide importer

Create file formats (i.e., plug-in configurations) for importing reporters. The formats marked as optional are not used in the test procedure, but may be useful to weed out import problems, since they allow importing all info from the raw data files. You may either enter the regular expressions as specified or use the "Test with file" feature.

Name Plugin Configuration values

Reporters for project A

Reporter importer

File	`mouse/ plates_and_reporters.mouse.v4.37k.txt`
Data header	384_number\t384_column\t384_row\t384_position\toligo_id.*
Data splitter	\t
Min data columns	5
Name	\oligo_id\
External ID	\oligo_id\
Description	\description_Ensembl*\
Gene symbol	\gene_symbol_Ensembl*\
Sequence	\oligo_sequence\

GenePix reporter importer
(optional)

Reporter importer

File	`mouse/ genepix.mouse.v4.37k.00h.gpr`
Data header	"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*
Data splitter	\t
Min data columns	48
Max data columns	48
Name	\Name\
External ID	\ID\

Reporters from Affymetrix annotations file

Reporter importer

File	`affymetrix/annotations/ MG_U74Av2_annot.csv.bz2`
Data header	"Probe Set ID","GeneChip Array".*
Data splitter	(?!"),(?=")
Name	\Probe Set ID\
External ID	\Probe Set ID\
Description	\Target Description\
Gene symbol	\Gene Symbol\

Reporters from GTF file

GTF Reporter importer

File	`sequencing/ UCSC_Human_hg19_RefSeqGenes.gtf.tar.bz2`
Data header	<seqname>\t.<transcript_id>.
Data splitter	\t
Min data columns	4
Remove quotes	yes
Complex mappings	allow
Name	\<transcript_id>\@\<seqname>\
External ID	\<transcript_id>\@\<seqname>\
Gene symbol	\<gene_id>\
Chromosome	\<seqname>\

Import reporters:
1. Go to the View -> Reporters page.
2. Click on the Import button.
3. Choose auto-detect and then upload the file plates_and_reporters.mouse.v4.37k.txt.
4. The Reporters for project A format should be found.
5. Select the skip option for the "Missing a required" value since the file contains rows with empty reporter ID:s.
6. Continue and wait for the import to finish. It should create 35,912 new reporters.
7. Repeat the procedure with the MG_U74Av2_annot.csv file. This time also select crop for the "String too long" setting since the file contains data that is too large for the datbase. 12,488 new reporters should be created.
8. Repeat the procedure with the UCSC_Human_hg19_RefSeqGenes.gtf file. The default error handling options can be used. This time 38,977 new reporters should be created.

4. Power user tests

The power user is the typical owner/administrator of a project. The power user sets up common resources used in the project, such as hardware, software, protocols, file formats and annotation types. In this case the power user is also responsible for managing the LIMS.

Create a project:

Name Members

Project A Groups: Group A (Use permission)
Activate the project.

Name	Members
Project A	Groups: Group A (Use permission)

Create annotation types [A] and protocol parameters [P]:

Name	Type	Unit	Interface	Values	Item types
Drug resistance [A]	String	-	radiobuttons	high, medium, low	Biosource
Time [A]	Integer	Hour	text box	-	Sample
RIN [A]	Float	-	text box	-	Extract
Dye swap [A]	Boolean	-	-	-	Raw bioassay
PMT gain [P]	Float	Volt (Electric potential)	-	-	Derived bioassay

Create item subtypes:

Name Item type Push annotations to parent

Quality control Extract Yes

Name	Item type	Push annotations to parent
Quality control	Extract	Yes

Create protocols (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):

Name	Type	Comment
Sampling A	Sampling
Extraction A	Extraction
Labeling A	Labeling
Library preparation A	Library preparation
Hybridization A	Hybridization
cBot Settings A	Cluster generation
Scanning A	Scanning	Select 'PMT gain' as a protocol parameter.
HiSeq Settings A	Sequencing
TopHat Settings A	Alignment
Feature extraction A	Feature extraction
Cufflinks Settings A	Feature extraction
Printing A	Printing

Create hardware (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):

Name	Type
Hybridization station A	Hybridization station
cBot A	Cluster generator
HiSeq 2000 A	Sequencer
Scanner A	Scanner
Print robot A	Print robot

Create software (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):

Name Type

Software A Feature extraction
Create a reporter clone template:

Name Properties

Template A External ID, ID, Version, Sequence, Gene symbol
Create bioplate type:

Name Biomaterial type Well lock mode

Bioplate type A Any Unlocked

Name	Type
Software A	Feature extraction

Name	Properties
Template A	External ID, ID, Version, Sequence, Gene symbol

Name	Biomaterial type	Well lock mode
Bioplate type A	Any	Unlocked

Create file formats (i.e., plug-in configurations). The formats marked as optional are not used in the test procedure, but may be useful to weed out import problems, since they allow importing all info from the raw data files. You may either enter the regular expressions as specified or use the "Test with file" feature.

Name Plugin Configuration values

Plates for project A

Plate importer

File	`mouse/ plates_and_reporters.mouse.v4.37k.txt`
Data header	384_number\t384_column\t384_row\t384_position\toligo_id.*
Data splitter	\t
Min data columns	5
Plate number/name	\384_number\
Row	\384_row\
Column	\384_column\
Reporter ID	\oligo_id\

GenePix feature importer
(optional)

Reporter map importer

File	`mouse/ genepix.mouse.v4.37k.00h.gpr`
Data header	"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*
Data splitter	\t
Min data columns	48
Max data columns	48
Reporter ID	\ID\
Block	\Block\
Column	\Column\
Row	\Row\

GTF features for project A

GTF reporter map importer

File	`sequencing/ UCSC_Human_hg19_RefSeqGenes.gtf`
Data header	<seqname>\t.<transcript_id>.
Data splitter	\t
Min data columns	4
Remove quotes	yes
Complex mappings	allow
Reporter ID	\<transcript_id>\@\<seqname>\
Feature ID	\<transcript_id>\@\<seqname>\

Raw data for project A

Raw data importer

File	`mouse/ genepix.mouse.v4.37k.00h.gpr`
Raw data type	Genepix
Header	"(.+)=(.*)"
Data header	"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $532\/635$".
Data splitter	\t
Min data columns	48
Max data columns	48
Block	\Block\
Column	\Column\
Row	\Row\
X	\X\
Y	\Y\
Reporter ID	\ID\
Spot diameter	\Dia.\
Channel 1 foreground median	\F635 Median\
Channel 1 foreground mean	\F635 Mean\
Channel 1 foreground standard deviation	\F635 SD\
Channel 1 background median	\B635 Median\
Channel 1 background mean	\B635 Mean\
Channel 1 background standard deviation	\B635 SD\
Percent pixels within 1 standard deviation	\% > B635+1SD\
Percent pixels within 2 standard deviations	\% > B635+2SD\
Percent saturated pixels	\F635 % Sat.\
Channel 2 foreground median	\F532 Median\
Channel 2 foreground mean	\F532 Mean\
Channel 2 foreground standard deviation	\F532 SD\
Channel 2 background median	\B532 Median\
Channel 2 background mean	\B532 Mean\
Channel 2 background standard deviation	\B532 SD\
Percent pixels within 1 standard deviation	\% > B532+1SD\
Percent pixels within 2 standard deviations	\% > B532+2SD\
Percent saturated pixels	\F532 % Sat.\
Foreground pixels	\F Pixels\
Background pixels	\B Pixels\
Flags	\Flags\

Raw data for project A (dye-swap)

Raw data importer

File	`mouse/ genepix.mouse.v4.37k.00h.dyeswap.gpr`
Raw data type	Genepix
Header	"(.+)=(.*)"
Data header	"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $635\/532$".
Data splitter	\t
Min data columns	48
Max data columns	48
Block	\Block\
Column	\Column\
Row	\Row\
X	\X\
Y	\Y\
Reporter ID	\ID\
Spot diameter	\Dia.\
Channel 1 foreground median	\F532 Median\
Channel 1 foreground mean	\F532 Mean\
Channel 1 foreground standard deviation	\F532 SD\
Channel 1 background median	\B532 Median\
Channel 1 background mean	\B532 Mean\
Channel 1 background standard deviation	\B532 SD\
Percent pixels within 1 standard deviation	\% > B532+1SD\
Percent pixels within 2 standard deviations	\% > B532+2SD\
Percent saturated pixels	\F532 % Sat.\
Channel 2 foreground median	\F635 Median\
Channel 2 foreground mean	\F635 Mean\
Channel 2 foreground standard deviation	\F635 SD\
Channel 2 background median	\B635 Median\
Channel 2 background mean	\B635 Mean\
Channel 2 background standard deviation	\B635 SD\
Percent pixels within 1 standard deviation	\% > B635+1SD\
Percent pixels within 2 standard deviations	\% > B635+2SD\
Percent saturated pixels	\F635 % Sat.\
Foreground pixels	\F Pixels\
Background pixels	\B Pixels\
Flags	\Flags\

Annotate the file formats:

File format Annotation Value

Raw data for project A Dye swap false

Raw data for project A (dye swap) Dye swap true

This will make the raw data importer automatically annotate the raw bioassays with the specified annotations.
Create plate type:

Name Geometry

Plate type A 384-well (16 x 24)
Import plates:
1. Go to the Array LIMS -> Plates page.
2. Click on the Import button.
3. Choose auto-detect and select the file plates_and_reporters.mouse.v4.37k.txt.
4. The Plates for project A format should be found.
5. Specify the following parameters:
  
  Plate type Plate type A
  
  Plate name prefix Plate A
  
  Plate name padding 4
6. Continue and wait for the import to finish. It should create 96 plates.

File format	Annotation	Value
Raw data for project A	Dye swap	false
Raw data for project A (dye swap)	Dye swap	true

Name	Geometry
Plate type A	384-well (16 x 24)

Create array designs and upload data files to them. Keep the 'Set as project default' option checked if doing this manually.

Name	Platform/Variant	File(s)
Array design A	Generic	Print map: `mouse/printmap.mouse.v4.37k.tam`
Affymetrix A	Affymetrix	CDF file: `affymtrix/cdf/MG_U74Av2.cdf`
RefSeqDesign A	Sequencing/Expression-like	GTF ref-seq file: `sequencing/UCSC_Human_hg19_RefSeqGenes.gtf`

Import array designs with the ArrayDesignImporter plug-in.

Make sure the data-files, mentioned in table above, are located in /home/power/, upload them if not
Click on the Import button on the array design list page.
Choose ArrayDesignImporter in the plug-in drop-down list.
Test with file: arraydesign_out.txt and set the parsing parameters with help of the Auto generate button on the Column mapping tab.
Start the import-job by clicking on the Finish button on the third wizard-page.

Connect Array design A with plates. Select the imported plates (plate names starting with Plate A) and sort them in the correct order (as indicated by their names).
Import features to Array design A:
1. Click on the Import button when viewing properties for the array design.
2. Choose auto-detect and use the file printmap.mouse.v4.37k.tam.
3. The Print map importer plug-in should be found.
4. Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.
Import features to RefSeqDesign A:
1. Click on the Import button when viewing properties for the array design.
2. Choose auto-detect and use the file UCSC_Human_hg19_RefSeqGenes.gtf.
3. The GTF reporter map importer plug-in should be found. Select the GTF features for project A format.
4. Continue and wait for the import to finish. It should create 38,977 features and 1 block.

Set project defaults. Go to the projects page and edit the Project A project. On the Defaults tab, set the following defaults. NOTE! Most of the items in this list should already be registered as default items if the 'Add as project default' option was used when creating the new items.

Setting	Value(s)
Raw data type	Genepix
Platforms	Generic Affymetrix
Platforms variants	Sequencing / Expression-like
Array designs	Array design A Affymetrix A RefSeqDesign A
Protocols	Sampling A Extraction A Labeling A Library preparation A Hybridization A cBot Settings A Scanning A HiSeq Settings A TopHat Settings A Feature extraction A Cufflinks Settings A Printing A
Hardware	Hybridization station A cBot A HiSeq 2000 A Scanner A Print robot A
Software	Software A TopHat Cufflinks

Create array batches:

Name Array design Print robot Protocol

Array batch A Array design A Print robot A Printing A

Affymetrix batch A Affymetrix A

Or
Import array batches with the ArrayBatchImporter plug-in.
1. Click on the Import button on the array batch list page.
2. Select ArrayBatchImporter in the plug-in drop-down list and click Next
3. Test with file: arraybatch_out.txt and set the parsing parameters with help of the Auto generate button on the Column mapping tab.
4. Start the import-job by clicking on the Finish button on the third wizzard-page.
Create array slides with the Create slides wizard.

Name Array batch Quantity

Array slide A. Array batch A 4

Affymetrix slide A. Affymetrix batch A 3

Or
Import array slides with the ArraySlideImporter plug-in.
1. Click on the Import button on the array slide list page.
2. Select ArraySlideImporter in the plug-in drop-down list and click Next
3. Test with file: arrayslide_out.txt and set the parsing parameters with help of the Auto generate button on the Column mapping tab.
4. Start the import-job by clicking on the Finish button on the third wizzard-page.

Name	Array design	Print robot	Protocol
Array batch A	Array design A	Print robot A	Printing A
Affymetrix batch A	Affymetrix A

Name	Array batch	Quantity
Array slide A.	Array batch A	4
Affymetrix slide A.	Affymetrix batch A	3

5. User tests

The user is a typical worker in the project. The user does the actual experimentation in the lab, which includes collecting samples, doing extraction, labeling and hybridizations. The user also scans and analyses the raw data resulting from the images. Inserting items can be done in two different ways, .

First step

Activate the Project A project.
Create a bioplate:

Name Plate geometry Bioplate type

Bioplate A 96-well (8 x 12) BioPlate type A
Continue with the second step, which can be done with batch importers or manually.

Name	Plate geometry	Bioplate type
Bioplate A	96-well (8 x 12)	BioPlate type A

Second step (using batch importers)

Click on the Import button on the list page.
Select <itemtype>Importer in the plug-in drop-down list and click Next

Test with file: using the right file(listed below) and set the parsing parameters by using the Auto generate button on the Column mapping tab.

Itemtype	File
Biosource	biosource_out.txt
Samples	sample_out.txt
Extracts (including labeled extracts and libraries)	extract_out.txt
Physical bioassays (hybridizations, flow cells)	physicalbioassay_out.txt
Derived bioassays (scans, assemblys)	derivedbioassay_out.txt
Raw bioassays	rawbioassay_out.txt

The files listed for biosource, samples, extracts, and derived bioassays also contain annotations for the items and these files should also be used with the annotation importer. The procedure is the same as for batch importers except that only \Name\ is needed in the column mapping. The annotation column should be selected by default in the second wizard-step.

Start the import-job by clicking on the Finish button on the third wizard-page.
Continue with the third step.

Second step (create items manually)

Create a biosource:

Name Annotations

Biosource A

Drug resistance: medium

Create samples:

Name

Protocol

Biosource

Bioplate [well]

Annotations

Sample A.00h

Sampling A

Biosource A

Bioplate A [A1]

Time:

Sample A.24h

Sampling A

Biosource A

Bioplate A [A2]

Time:

24h

Sample A.ref

Sampling A

Bioplate A [A3]

Create extracts:

Name

Type

Protocol

Parent

Bioplate [well]

Annotations

Extract A.00h

Extraction A

Sample A.00h

Bioplate A [B1]

Extract A.24h

Extraction A

Sample A.24h

Bioplate A [B2]

Extract A.ref

Extraction A

Sample A.ref

Bioplate A [B3]

Extract A.00h.qc

Quality control

Extract A.00h

RIN:

8.1

Extract A.24h.qc

Quality control

Extract A.24h

RIN:

8.5

Extract A.ref.qc

Quality control

Extract A.ref

RIN:

9.2

Create labeled extracts and libraries:

Name	Type	Label	Protocol	Extract	Bioplate [well]
Labeled extract A.00h	Labeled extract	cy3	Labeling A	Extract A.00h	Bioplate A [C1]
Labeled extract A.24h	Labeled extract	cy3	Labeling A	Extract A.24h	Bioplate A [C2]
Labeled extract A.ref	Labeled extract	cy5	Labeling A	Extract A.ref	Bioplate A [C3]
Labeled extract A.00h (dye-swap)	Labeled extract	cy5	Labeling A	Extract A.00h	Bioplate A [D1]
Labeled extract A.24h (dye-swap)	Labeled extract	cy5	Labeling A	Extract A.24h	Bioplate A [D2]
Labeled extract A.ref (dye-swap)	Labeled extract	cy3	Labeling A	Extract A.ref	Bioplate A [D3]
Library A.00h	Library	-	Library preparation A	Extract A.00h	Bioplate A [E1]
Library A.24h	Library	-	Library preparation A	Extract A.24h	Bioplate A [E2]

Create physical bioassays (hybridizations and flow cells):

Name	Protocol	Hardware	Array slide	Extracts (position)
Hybridization A.00h	Hybridization A	Hybridization station A	Array slide A.1	Labeled extract A.00h, Labeled extract A.ref
Hybridization A.24h	Hybridization A	Hybridization station A	Array slide A.2	Labeled extract A.24h, Labeled extract A.ref
Hybridization A.00h (dye-swap)	Hybridization A	Hybridization station A	Array slide A.3	Labeled extract A.00h (dye-swap), Labeled extract A.ref (dye-swap)
Hybridization A.24h (dye-swap)	Hybridization A	Hybridization station A	Array slide A.4	Labeled extract A.24h (dye-swap), Labeled extract A.ref (dye-swap)
Affymetrix hyb A.1	Hybridization A	Hybridization station A	Affymetrix slide A.1	Labeled extract A.00h
Affymetrix hyb A.2	Hybridization A	Hybridization station A	Affymetrix slide A.2	Labeled extract A.24h
Affymetrix hyb A.3	Hybridization A	Hybridization station A	Affymetrix slide A.3	Labeled extract A.ref
Flow cell A	cBot Settings A	cBot A	-	Library A.00h (1), Library A.24h (2)

Create derived bioassays (scans, arrangements, etc.):

Name	Parent bioasasay	Parent extract	Hardware/Software	Protocol	PMT gain
Scan A.00h	Hybridization A.00h	-	HW: Scanner A	Scanning A	400 V
Scan A.24h	Hybridization A.24h	-	HW: Scanner A	Scanning A	500 V
Scan A.00h (dye-swap)	Hybridization A.00h (dye-swap)	-	HW: Scanner A	Scanning A	600 V
Scan A.24h (dye-swap)	Hybridization A.24h (dye-swap)	-	HW: Scanner A	Scanning A	700 V
Affymetrix scan A.1	Affymetrix hyb A.1	-	HW: Scanner A	Scanning A	800 V
Affymetrix scan A.2	Affymetrix hyb A.2	-	HW: Scanner A	Scanning A	900 V
Affymetrix scan A.3	Affymetrix hyb A.3	-	HW: Scanner A	Scanning A	1000 V
Sequenced A	Flow cell A	-	HW: HiSeq 2000 A	HiSeq Settings A	-
Arrangement A.00h	Sequenced A	Library A.00h	SW: TopHat	TopHat Settings A	-
Arrangement A.24h	Sequenced A	Library A.24h	SW: TopHat	TopHat Settings A	-

Create raw bioassays:

Name	Platform/Raw data type	Parent bioassay	Parent extract	Array design	Protocol	Software	File(s)
Raw bioassay A.00h	Generic/GenePix	Scan A.00h	-	Array design A	Feature extraction A	Software A	Raw data: `mouse/genepix.mouse.v4.37k.00h.gpr`
Raw bioassay A.24h	Generic/GenePix	Scan A.24h	-	Array design A	Feature extraction A	Software A	Raw data: `mouse/genepix.mouse.v4.37k.24h.gpr`
Raw bioassay A.00h (dye-swap)	Generic/GenePix	Scan A.00h (dye-swap)	-	Array design A	Feature extraction A	Software A	Raw data: `mouse/genepix.mouse.v4.37k.00h.dyeswap.gpr`
Raw bioassay A.24h (dye-swap)	Generic/GenePix	Scan A.24h (dye-swap)	-	Array design A	Feature extraction A	Software A	Raw data: `mouse/genepix.mouse.v4.37k.24h.dyeswap.gpr`
Affymetrix raw A.1	Affymetrix	Affymetrix scan A.1	-	Affymetrix A	Feature extraction A	Software A	CEL file: `affymetrix/E-TEST-1.ebi.ac.uk/jos1761.cel`
Affymetrix raw A.2	Affymetrix	Affymetrix scan A.2	-	Affymetrix A	Feature extraction A	Software A	CEL file: `affymetrix/E-TEST-1.ebi.ac.uk/jos1762.cel`
Affymetrix raw A.3	Affymetrix	Affymetrix scan A.3	-	Affymetrix A	Feature extraction A	Software A	CEL file: `affymetrix/E-TEST-1.ebi.ac.uk/jos1763.cel`
SeqRaw A.00h	Sequencing/Expression-like/Cufflinks	Arrangement A.00h	Library A.00h	RefSeqDesign A	Cufflinks Settings A	Cufflinks	FPKM tracking file: `sequencing/dataset1_norm1/isoforms.fpkm_tracking`
SeqRaw A.24h	Sequencing/Expression-like/Cufflinks	Arrangement A.24h	Library A.24h	RefSeqDesign A	Cufflinks Settings A	Cufflinks	FPKM tracking file: `sequencing/dataset2_norm1/isoforms.fpkm_tracking`

Third step

Create experiments:

Name	Raw data type	Raw bioassays	Experimental factors
Experiment A	GenePix	Raw bioassay A.00h, Raw bioassay A.24h, Raw bioassay A.00h (dye-swap), Raw bioassay A.24h (dye-swap)	Drug resistance, Time, RIN, Dye swap, PMT gain
Affymetrix A	Affymetrix	Affymetrix raw A.1, Affymetrix raw A.2, Affymetrix raw A.3	Drug resistance, Time, RIN, PMT gain
Sequence A	Cufflinks	SeqRaw A.00h, SeqRaw A.24h	Drug resistance, Time, RIN

Import raw data to the Genepix and Cufflinks raw bioassays. There are two possible ways to do this:

Manually import to each raw bioassay.
Batch import to multiple raw bioassays.

Manual import: Go to the properties tab for each raw bioassay. Click on the Import button and use the auto-detect feature to import the raw data. Use the default configuration values except for those listed in the table below.

Batch import: The batch import is started from the properties tab of the experiment. Click on "Import" and use the auto-detect feature with one of the files from the raw bioassays. Use the default configuration values except for those listed in the table below. The batch import should import two raw data sets in one go (since it can only work with a single file format at a time and the dye-swap files uses a different file format). Repeat the batch import a second time to import the remaining two raw data sets.

Parameter	Value	Mode
Feature mismatch	smart	both
Invalid numeric value	null	both
Log file	~/import.log	batch import

In both cases, the import should produce the same results as in the table below. When using the batch import mode, the detailed information for each raw bioassay is only found in the log file.

Raw bioassay	Raw data file	Spots inserted/with null reporter/skipped)	Annotations created
Raw bioassay A.00h	genepix.mouse.v4.37k.00h.gpr	36,864/632/768	Dye swap: false
Raw bioassay A.24h	genepix.mouse.v4.37k.24h.gpr	36,864/632/768	Dye swap: false
Raw bioassay A.00h (dye-swap)	genepix.mouse.v4.37k.00h.dyeswap.gpr	36,864/632/768	Dye swap: true
Raw bioassay A.24h (dye-swap)	genepix.mouse.v4.37k.24h.dyeswap.gpr	36,864/632/768	Dye swap: true
SeqRaw A.00h	dataset1_norm1/isoforms.fpkm_tracking	38,293/0/0	-
SeqRaw A.24h	dataset2_norm1/isoforms.fpkm_tracking	38,293/0/0	-

Inherit the annotations from the scans, extracts, samples and biosource for each root raw bioassay. Use the auto-inherit function that exists on the experiment properties tab. Make sure that all experimental factors are selected by the check boxes, then click on the Auto-inherit link in the column header. Use the Inherit option for some annotations and Clone option for some. Uncheck the No duplicates option for the RIN annotation (see note 2 below).
Note! The Affymetrix raw A.3 data set is missing biomaterial parents with annotations.
Note 2! In Experiment A there are duplicate values for the RIN annotations. Verify and fix this by manually removing the annotations that are inherited from the Extract A.ref.qc extract (value=9.2).

Check the experiment overview page and use the Validate function for each of the three experiments.

For the Experiment A experiment, it should display several warnings about missing kits and one warning about a missing biosurce on the reference sample.

The Affymetrix A experiment gives some more warnings. Most of them are related to not using the project default items, missing protocols and missing hardware. There should also be an error about missing experimental factor values for the Affymetrix.3 raw bioassay. It is expected since this comes from the reference sample which doesn't have values for those annotations. The warnings about the number of spots mismatch is expected since the array design count probesets, while the raw bioassays count probes.

The Sequence A experiment also has some missing items, and a different raw data type for the experiment and raw bioassays.

Change validation options to reduce the number of warnings:

Validation option	Setting
Project defaults	Set all to `Ignore`
Missing items	Set all to `Ignore`
Annotations - Missing factor value	`Warning`
Other - Raw spots <> features	`Ignore`

After the changes there should now only be two warnings about the missing factor values for the Affymetrix experiment and no warnings at all for the other experiments.

6. Analysis tests

Now it is time to analyse the data. The analysis test should be done by both a regular user and a guest.

Activate the Project A project
Go to the Experiment A experiment.
Clone the reporters:

Clone template Clone source

Template A Raw data

Click on "Next" and wait for the plug-in to finish. It should report that 35,912 reporters has been cloned.
Switch to the "Bioassay sets" tab. Create a new root bioassay set:

Bioassay set name Raw bioassays Formula

Root bioassay set all Mean FG - Mean BG

Wait for the plug-in to finish.
Select the created bioassay set and create a filtered bioassayset:

Child name Filter preset Expression

Filtered bioassay set - ch(1) > 0 && ch(2) > 0 && rep('id') != null

Wait for the plug-in to finish. It should report that 136,498 spots remain and that 10,958 spots has been removed.
Select the filtered bioassay set and run a normalization plug-in:

Plugin Parameters

Normalization: Lowess Accept the default parameters.

Wait for the plug in to finish. It should report that 136,498 spots has been normalized and 0 spots has been removed.
Select the normalized bioassay set and check the MA plots and the correction factor plots. Here are four examples:

MA plots Correction factor plots

Clone template	Clone source
Template A	Raw data

Try the plot tool with the following plots. Use the Save function to save one them as a file in the BASE file system, and the Download function to download a plot to your computer.

Plot type

Y-axis preset

X-axis preset

Other options

Scatter plot

M, log2(ch1 / ch2)

A, log10(ch1 * ch2) / 2

Histogram plot

Count

Ratio, ch1 / ch2

Log scale	checked
Bin size	0.1
Annotation	Time

Here are two examples:

Scatter plot

Histogram plot

Plate type	Plate type A
Plate name prefix	Plate A
Plate name padding	4