Hello,
I am trying to reproduce the analysis done in Chapter 18 ("Profiles of Unrelated Nigerian Individuals") present in the Limma User's guide. I typed the commands described and I got the same genes differentially expressed between male and females. Here you go the first row of tapTable command:
Symbol Chr logFC AveExpr t P.Value adj.P.Val B
ENSG00000229807 XIST X -9.857 3.8076 -32.5 1.21e-44 2.10e-40 66.5
I would like to get the mean expression in male and female group, so I take a look at v$E matrix (where v is the voomed object and v$E contains the normalized values of the genes in my samples) and first of all I calculate the mean expression of XIST among the samples. It matches (3.8076) with the one reported by topTable. Then, I calculate the mean of expression in male and female group and the fold change as mean_male - mean_female, but I got a slightly different FC from the one reported by topTable:
My calculation FC: -9.815
topTable log2FC: -9.857
Could you help me to figure out this difference? Is Limma supposed to calculate the logFC as mean_group1 - mean_group2 because the values are logged?
Best,
Luciano
http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
Is it possible this is due to rounding error? You're only seeing a certain number of decimal places in your output, and limma has more available.
logFC = mean_group1 - mean_group2 because it is logged. If you want to do division in log space, subtract. If you want multiplication, add the values.
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