Hello,

Apologies in advance for the question-I am trying to make sense of RNA Seq and the stats behind it.

I am looking to use the transformed counts from DESeq2 as input to WGCNA. Since we are using a design when we create the DESeqDataSetFromMatrix before we get the counts (and depending on the factor/ combination of factors we use the counts slightly change), I was wondering if this would affect how WGCNA will correlate the modules with different traits (that might not be in the initial design).

An example:

I am trying to get transformed data counts using ~time_to_rebound (continuous variable, cut in 3 bins). In WGCNA I would like to see what modules correlate with age, time to rebound (as a continuous variable) and groupings of patients based on time to rebound but in different cut-offs.

Don't know if I making sense here but any help/ advice would be much appreciated!!

Thank you!!

Penny

Dear Penny,

From the DESeq2 side, the scaled counts (counts(dds, normalized=TRUE)) depend on the size factors. These depend on the samples included in the dataset but not on the design.