Job Number: 385797

[Daryl Griffin]

Hi, 

Im receiving the following error when trying to VoomNormalise my data (Job Number: 385797):

Error in if (fit$rank < ncol(design)) { : argument is of length zero Calls: GP.preprocess.read.counts -> voom Execution halted

Can you assist please. Im doing this so i can use the DESeq2 module but the data used was brought in using GEOIMporter:Job Number 385323.  Is there another way to import it so its in a ready format for DESeq2 analysis?

Best,

Daryl

[Anthony Castanza]

Hi Daryl,

 

This dataset is from a microarray platform (GSE72865 is tagged as Platform: GPL10558 Illumina HumanHT-12 V4.0 expression beadchip) and not a sequencing based one. The both Voom and DESeq2 expect counts from RNA-seq so Voom failing is expected, and DESeq2 should as well (or would return a non-statistically valid result). I believe that the correct module to analyze this data would be the ComparativeMarkerSelection tool, but any of my colleagues here can feel free to chime in and correct me.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "GenePattern Help Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genepattern-he...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/e05074e3-c254-4c9a-bde4-8823021fead5n%40googlegroups.com.