Dear Colleagues,

I have an RNA-seq library with 27 samples. 9 of these samples are what we
call input as the other 18 are derived from them through a biochemical
process. As such, I have already scaled the genes in those 18 samples to
roughly add-up to the corresponding inputs.

To manage this at the calcNormFactors step I have the following code:
y$samples
y_inputs=y$counts[,grep(".[i]..",colnames(y$counts))]
norm_factor_inputs <- calcNormFactors(y_inputs)
y$samples$norm.factors[grep(".[i]..",row.names(y$samples))] =
norm_factor_inputs
y$samples$norm.factors[grep(".[p]..",row.names(y$samples))] =
norm_factor_inputs
y$samples$norm.factors[grep(".[r]..",row.names(y$samples))] =
norm_factor_inputs
y$samples

So what I'm basically trying to do is calcNormFactors for just the inputs
and then copy them to be the NormFactors for the p and r samples. Is
copying them like this telling edgeR to re-compute the library sizes? It
doesn't seem to be happening because the lib.size before and after these
commands are the same.

Best,
Scott Daniel
Zarnescu Lab
MCB Ph.D. Program
University of Arizona

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