My aim is to use a (kallisto|salmon)/tximport/DESeq2 pipeline using length-corrected gene count estimates.
The tximport vignette provides two methods for importing gene-level counts for DGE (differential gene expression), namely:
Namely, the “original counts and offset” method and the “bias corrected counts without an offset”.
I am fine, with the former, but am having difficulties with the latter.
For the latter method, the tximport vignette advises the following:
"The second method is to use the tximport argument countsFromAbundance="lengthScaledTPM" or "scaledTPM", and then to use the gene-level count matrix txi$counts directly as you would a regular count matrix with these software"
For DESeq2, I took this to mean taking txi$counts and then passing this object as the first argument to
DESeqDataSetFromMatrix. However, an error relating to the use of non-integer values in txi$counts results.
So my problem is this: I am not sure if I were to use estimated counts from kallisto/salmon, how I could bias-correct the estimated counts using tximport, and then to use the result as a regular count matrix as suggested by the tximport vigenette, given that matrix values will be non-integer - and unsuitable for use with
Apologies in advance, if I have misunderstood something here.