I currently am using a dataset with 5 timepoints and 4 replicates per timepoint. While the results file exports the L2FC, I am also interested in extracting the numerator log2 values for each time point. I have already extracted the log2 normalized counts for each individual sample with the code below, but am unable to find a way to extract the log2 mean normalized counts for each level/ timepoint.
|1 hr||1 hr||1 hr||1 hr||2 hr||2 hr||2 hr||2 hr|
|Gene A norm cts||100||110||100||150||300||350||400||320|
1 hr average= 115
2 hr average = 342.5
log2 normalized counts per level/ timepoint
1 hr: log2(115+1)
2 hr: log2(342.5+1)
Is there a simple way to do this in the R package? Otherwise, would I have to manually calculate like outlined above?
# Define DE design dds = DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~timepoint) dds$timepoint=relevel(dds$timepoint, ref="0 hrs") # Run the DESeq pipeline dds = DESeq(dds, test="LRT", full=~timepoint, reduced=~1) res=results(dds, alpha=0.05) resSig=subset(res, padj<0.05) # Extract log2 shifted normalized counts per sample l2normcts=counts(dds, normTransform=TRUE)