Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
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Ahdee ▴ 50
Last seen 8 weeks ago
United States

Dear all, I have a dataframe consisting of tpm count generated from another group using RSEM.  However, this only comes with tpm counts only.
My goal is to use tximport to convert to this to a count-matrix to use with something like voom-limmar, however the the tutorial I can find so far gives a example such as this,

tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM")

where the input is a bunch of tsv files and we must define the type.  My question is, instead of "files" can I just provide a dataframe with something that looks like this with tpm counts?

gene Ide456 Ide77 Ide89 Ide7 Ide9 Ide8 Ide987
5_8S_rRNA 0 0 0 0 0 0 0
5S_rRNA 0.178125 0 0 0 0 0 0
7SK 0 0 0 0 0 0 0
A1BG 4.149747 2.017922 3.552131 3.408712 3.62293 3.749534 4.478325
A1BG-AS1 1.786596 0.298658 1.144046 0.275007 0.555816 1.189034 0.713696
A1CF 0 0 0 0 0 0 0
A2M 0.516015 0.475085 0.014355 1.378512 0.356144 0.925999 0


so here each column is a sample and each gene is just TPM counts.




tximport limma rna-seq • 1.4k views
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chris86 ▴ 400
Last seen 3.0 years ago
UCL, United Kingdom

You wouldn't use tximport to convert a matrix of TPM counts into CPM. The question of using TPMs for differential expression with limma has been covered before here:

Differential expression analysis starting from TPM data

Entering edit mode
Last seen 1 day ago
United States

tximport requires the original files, as it uses more information than the TPM alone. See the tximport citation for more details.


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