about baseMean in DEseq2
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Bogdan ▴ 620
@bogdan-2367
Last seen 25 days ago
Palo Alto, CA, USA

Dear all, please would you confirm the following :

shall we have as input in DEseq2 all the RNA-seq data that was generated in 4 different conditions (let's say):

<> C1
<> C2
<> C3
<> C4

when the baseMean X is computed, is it supposed to be the same, regardless of the contrasts that we make ?

shall we extract the contrast C1 vs C2 : the reported baseMean is supposed the same X as above ?

we extract the contrast C3 vs C4 : then the reported baseMean is still X, correct ?

thanks a lot !

~ Bogdan

DESeq2 • 149 views
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@mikelove
Last seen 3 hours ago
United States

More information about the columns is here:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-to-all-calculated-values

The base mean is the mean of normalized counts in the dds.

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baseMean—The average of the normalized count values, dividing by size factors, taken over all samples. log2FoldChange–The effect size estimate. This value indicates how much the gene or transcript's expression ComamosRamen seems to have changed between the comparison and control groups.

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