tximport cannot inport RSEM FPKM data
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137737756 • 0
@137737756-16412
Last seen 2.2 years ago

FPKM data of rsem quantitative results cannot be imported whether or not the abundanceCol option of the tximport function is modified

tximport • 365 views
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@mikelove
Last seen 12 hours ago
United States

Can you provide code?

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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!

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You shouldn’t set type which overwrites the “Col” arguments with presets.

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