Question: Biased results of DESeq2 LRT (Group name order)
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gravatar for minyoungcho93
7 weeks ago by
minyoungcho930 wrote:

Hello,

I am using DESeq2 to perform LRT analysis. I have 4 conditions, and each group named Group1, Group2, Group3, and Group4. Each group has 80 to 100 samples. I use only p-adj value to determine DEGs.

Whenever I use DESeq2 with LRT function, the last group (like group4) has distinctive characteristics. When I changed the group name (group3 to group4, group4 to group3), DEGs were changed. (common DEGs were only 1/4 or 1/5)

Should I use other values to determine DEGs except for p-adjust value? Or should I change the design or other codes?

DESeq2Table <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ Group_Name) DESeq2Table <- DESeq(DESeq2Table, test="LRT", reduced=~1)

DESeq2Table <- estimateSizeFactors(DESeq2Table) DESeq2Table <- estimateDispersions(DESeq2Table)

DESeq2Table <- nbinomWaldTest(DESeq2Table) DESeq2Res <- results(DESeq2Table, pAdjustMethod = "BH")

Thanks,

deseq2 • 64 views
ADD COMMENTlink modified 7 weeks ago by Michael Love26k • written 7 weeks ago by minyoungcho930
Answer: Biased results of DESeq2 LRT (Group name order)
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gravatar for Michael Love
7 weeks ago by
Michael Love26k
United States
Michael Love26k wrote:

Above you have code for the Wald test, is this on purpose? Do you know that you’re doing pairwise comparisons?

You should remove these lines:

DESeq2Table <- estimateSizeFactors(DESeq2Table) DESeq2Table <- estimateDispersions(DESeq2Table) DESeq2Table <- nbinomWaldTest(DESeq2Table)

ADD COMMENTlink written 7 weeks ago by Michael Love26k

Thanks for the reply! I'll try it again.

ADD REPLYlink written 7 weeks ago by minyoungcho930
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