Affy MTA_1.0 CEL conversion to GCT

Josh Spin

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Apr 10, 2020, 7:44:22 PM4/10/20

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Complete description of the problem (ie what you were trying to do and what went wrong):

Hi folks. Trying to convert some CEL files from Affymetrix Mouse Transcriptome Array 1.0 to GCT format so I can use the BROAD GSEA tool.

This array used to be called the GeneChip® Mouse Exon 1.0 ST Array, was renamed to Affymetrix Mouse Transcriptome Array 1.0, and has again been renamed by Thermo-Scientific and is now called Clariom D. Notably the CEL files still identify the arrays as MTA 1.0.

I tried running the job on both the AffySTExpressionFileCreator and the ExpressionFileCreator and got errors on both not recognizing the MTA arrays. The stderr.txt outputs are below.

Since all ST arrays are being renamed this way, this should be a global issue.

Ideas for making this work?

Thanks.

Job ID if run on a publicly available server.

221365

221364

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.

Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:

For AffySTExpressionFileCreator:

"Error in GP.affyst.efc(files.to.process, normalize, background.correct,  : 
  Array type MTA-1_0 does not seem to be an ST array.  You may want to check whether it is supported by ExpressionFileCreator instead.
Calls: tryCatch -> tryCatchList -> GP.affyst.efc
Execution halted"

For ExpressionFileCreator:

"Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain MTA-1_0
Library - package mta10cdf not installed
Bioconductor - mta10cdf not available
Calls: parseCmdLine ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo
Execution halted"