Opened 17 years ago

Closed 17 years ago

#467 closed defect (fixed)

GPR import problem

Reported by: base Owned by: Johan Enell
Priority: major Milestone: BASE 2.2
Component: web Version: 2.1.1
Keywords: gpr Cc:


Hello, I couldn't use neither the Cy5/cy3 gpr import plugin or the Cy3/cy5 plugin. I checked and found out that there was a problem in the plugin configuration. The wavelengths of the dyes are inversed. cy5 = 635 whereas cy3=532

So the data header line for Cy3/CY5 should look like this:

"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(532\/635\)".*

whereas the data header line for the Cy5/Cy3 should look like this:

"Block"\t"Column"\t"Row"\t"Name"\t"ID".*"Ratio of Medians \(635\/532\)".*

This fixed the problem. That's it.

Change History (2)

comment:1 by base, 17 years ago

Ooops, I forgot to add another change to the Cy5/Cy3 plugin. Both the columns RATIO SD and Log Ratio should be as follows.

\Ratios SD (532/635)\ \Log Ratio (532/635)\

\Rgn R2 (635/532)\ "The 2 must not be and exp number" . This one applies to both plugins.

Please check both plugins for consistency.

comment:2 by Nicklas Nordborg, 17 years ago

Milestone: BASE 2.1.2BASE 2.2
Resolution: fixed
Status: newclosed

This has already been fixed and will be included in the BASE 2.2 release.

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