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Last seen 3.8 years ago
FPKM data of rsem quantitative results cannot be imported whether or not the abundanceCol option of the tximport function is modified
I noticed the same thing, for instance the following three command lines:
txi.rsem <- tximport(all, type = "rsem", txIn = FALSE, txOut = FALSE)
txi.rsem.tpm <- tximport(all, type = "rsem", txIn = FALSE, txOut = FALSE,abundanceCol="TPM")
txi.rsem.fpkm <- tximport(all, type = "rsem", txIn = FALSE, txOut = FALSE,abundanceCol="FPKM")
lead to the same result (same counts and same abundance values), regardless of the option "abundanceCol" being set to TPM or FPKM. More precisely, counts correspond to "expected_count" column and "abundance" corresponds to the "TPM" column of the rsem.genes.results file.
How can I retrieve the FPKM values using tximport? thanks a lot!
You shouldn’t set
typewhich overwrites the “Col” arguments with presets.