New export format for bioassay set spot data

[Jari Häkkinen]

It would be nice to be able to export bioassay set spot data without actually listing the spot data. The listing is an expensive operation and is often not needed before exporting the data.

The new export could be an action in the experiment analysis tree. Currently there is an export action that allows the user to select predefined formats (BASEfile and MeV) but sometimes users want to select what they export. Is it possible to add the spot data export dialog as an option to this already existing export action?

[Nicklas Nordborg]

Do you mean the export that is done by the Table exporter plug-in? If so, it is not possible to export without first listing the table, because the table exporter depends on information that is gathered during the listing. It's more or less the same limitation that is discussed in #1128.

Does the table exporter offer more options than a serial BASEfile? Except for the obvious thing that it only add a simple header on the first line.

[Jari Häkkinen]

I suppose the BASEfile can do the trick, however there is the header and understanding it. The table exporter creates a plain vanilla tab separated file. Users like it for use in spreadsheets. One could imagine another export plug-in that behaves similarly to BASEfile export but that generates a table exporter. Would it be worth doing?

[Jari Häkkinen]

Replying to jari:

I suppose the BASEfile can do the trick, however there is the header and understanding it. The table exporter creates a plain vanilla tab separated file. Users like it for use in spreadsheets. One could imagine another export plug-in that behaves similarly to BASEfile export but that generates a table exporter. Would it be worth doing?

I could imagine that the user selects field to export, is allowed to select whether one big file with all data is exported or one file for each assay in the set (in a zip, tar, or similar).

In the case of one big file the column headers need to be concatenated with bioassay name and field name like MyAssay1_ch1, MyAssay1_xtravalue, MyAssay2_ch1, MyAssay2_xtravalue, ... The common columns can retain field names as column header.

For the multi-file export one could simply retain the field names as column headers, file names can be like MyAssay1.tsv, MyAssay2.tsv, ... Here I use .tsv as extension but maybe something else is more appropriate.