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Question: DeSeq Output results file: only one log2(FC) column but 4 treatments?
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gravatar for sf.rocha
20 days ago by
sf.rocha • 0
sf.rocha • 0 wrote:

Hi,

I'm trying to analyse RNAseq data from 4 samples (control, treatment A, treatment B, treatment C) and I don't really understand the information that is provided in the results output file:

GeneID Base mean log2(FC) StdErr Wald-Stats P-value P-adj

These are the columns that are on the file... I expected to obtain results on the fold change of each of the treated samples in relation to the control sample. Yet, this is not the case since I have only have one Log2(FC) column and no indication as to which samples it refers to.

I would appreciate feedback please.

Thank you.

deseq • 39 views
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modified 15 days ago by Jennifer Hillman Jackson ♦ 25k • written 20 days ago by sf.rocha • 0
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gravatar for Jennifer Hillman Jackson
15 days ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try using the option "Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)" set to Yes. By default (No), the results are combined.

More details (based on the line-command version of the tool) is here and most will apply to the Galaxy wrapped version of the tool: https://support.bioconductor.org/p/62927/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 15 days ago by Jennifer Hillman Jackson ♦ 25k
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