Hello DESeq community,

I wanted to ask how basemean and log2foldchange are calculated.

1) From mcol(mcol(dds_fit)), the basemean is denoted as "basemean over all rows". But I can't pin down what "all rows" this means. For a single transcript, my manual mean calculation of all counts across all replicates, all conditions do not equal to the DESeq reported basemean for a single transcript.

2) log2foldchange seems to be changing with the contrasting variable. This is a little surprising since I'd expect log2foldchange to be a static number when comparing two conditions, and the contrasting variables only dictate testing for significance, ie., p-value.

Thank you in advance.

-Rob
 		 	   		  
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