Error in basicRMA(pms, pnVec, normalize, background) :
Thibaut Matis
Anthony Castanza
Hello,
What tutorial are you referencing? The documentation supplys sample files but these are indented to be used as-is with the AffySTExpressionFileCreator module. The default behavior of the AffySTExpressionFileCreator module is to normalize, background correct, and annotate the dataset using its internal functions. It appears that you’ve already done this to the dataset manually. Because of this preprocessing, did you set the applicable parameters in the module to “no”? From the error message it appears that the module is attempting to normalize the data that you’ve already normalized, this would be expected to cause an error in order to prevent erroneous double normalization.
Let me know if this isn’t the case, or if you’re still having issues with the module,
-Anthony
Anthony S. Castanza, PhD
Mesirov Lab, Department of Medicine
University of California, San Diego
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Thibaut Matis
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Anthony Castanza
Could you send us the Job ID of one of the runs that returned this error so that we can investigate what might’ve gone wrong?
Thanks!
-Anthony
Anthony S. Castanza, PhD
Mesirov Lab, Department of Medicine
University of California, San Diego
From:
genepatt...@googlegroups.com <genepatt...@googlegroups.com> on behalf of Thibaut Matis <thibau...@gmail.com>
Date: Tuesday, February 23, 2021 at 1:48 PM
To: genepatt...@googlegroups.com <genepatt...@googlegroups.com>
Subject: Re: [genepattern-help:1771] Error in basicRMA(pms, pnVec, normalize, background) :
Hi! Thank you a lot for your reply!!
I'm talking about the Affymetrix documentation:https://www.genepattern.org/modules/docs/AffySTExpressionFileCreator/2. There are examples of input files at the bottom I used
I understand your point, so I reloaded the job without setting normalization once or without background as well, same issue with the same error message
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Thibaut Matis
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Anthony Castanza
Hi,
Thanks for bringing this to your attention. We use an externally sourced docker container to run this module, and it appears as if they silently pushed an update to the tag we target that modified the underlying operating system and caused the module to fail. We’re working on getting this fixed ASAP. In the meantime if you need to run Affymetrix arrays that are not based on the Clariom platform, the previous version of the module is available until we can get this version (that introduced clariom array support) back up and running.
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Thibaut MATIS
Interne d'Oncogénétique
Institut Bergonié - Bordeaux
email : t.m...@bordeaux.unicancer.fr
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