Detailed explanations for DEXSeq output columns
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@angel-liang-23540
Last seen 2.4 years ago

Hi, I have output results from DEXSeq using the DEXSeqDataSetFromHTSeq() method, but I can't find any detailed documentation which explains what the column names mean:

DEXSeqresults <- DEXSeqResults(DEXSeqDataSet) colnames(DEXSeqresults)

[1] "groupID" "featureID"
"exonBaseMean" "dispersion"
[5] "stat" "pvalue"
"padj" "control"
[9] "treat" "log2foldtreatcontrol" "genomicData.seqnames" "genomicData.start"
[13] "genomicData.end" "genomicData.width" "genomicData.strand" "countData.1"
[17] "countData.2" "countData.3"
"countData.4" "countData.5"
[21] "countData.6" "transcripts"
"comparison"

It's obvious that countData.x columns mean the raw input counts, but what about the "control" and "treat" columns for example? could they be logCPM values? what about "stat" and "exonBaseMean"?

Thanks in advance

DEXSeq • 548 views
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Alejandro Reyes ★ 1.8k
@alejandro-reyes-5124
Last seen 6 weeks ago
Novartis Institutes for BioMedical Reseā€¦

Thanks for your question Angel. You can find the details of each column in the metadata of the columns:

data(pasillaDEXSeqDataSet, package="pasilla")
dxd <- estimateSizeFactors( dxd )
dxd <- estimateDispersions( dxd )
dxd <- testForDEU( dxd )
dxr <- DEXSeqResults( dxd )
elementMetadata(dxr)

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thanks so much! i didn't know you could do that!

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