Question: tximport query for un-normalized and TPM data
0
gravatar for HKS
8 days ago by
HKS0
HKS0 wrote:

I am using .ctab files and type = "stringtie" to calculate txi$abundance, txi$counts, and since the .ctab file contains FPKM values, txi$abundance is giving FPKM matrix. But I want txi$abundance to contain TPM values, and also un-normalised raw counts.

I want two types of matrices txi$abundance to contain un-normalised or raw counts and another txi.tpm$abundance to contain TPM values, because I want to use the raw count matrix for DESeq analysis and TPM matrix for machine learning.

Is it possible with tximport?

tximport • 55 views
ADD COMMENTlink modified 8 days ago by Michael Love24k • written 8 days ago by HKS0
Answer: tximport query for un-normalized and TPM data
0
gravatar for Michael Love
8 days ago by
Michael Love24k
United States
Michael Love24k wrote:

tximport doesn’t convert Stringtie’s FPKM output to TPM but you can very easily using simple R. Just divide each column by its sum and multiply the matrix by 1e6.

ADD COMMENTlink written 8 days ago by Michael Love24k

Is this correct: TPMfromFPKM <- as.numeric(exp(log(txi$abundance) - log(sum(txi$abundance)) + log(1e6)))

But this is not giving the output in matrix form, rather the output has long column with values in just one coloumn for all samples.. I want it in matrix form..

ADD REPLYlink written 8 days ago by HKS0

You can try to work it out yourself. This is out of scope of tximport.

ADD REPLYlink written 8 days ago by Michael Love24k

yes, I solved it, Thank you..

ADD REPLYlink written 8 days ago by HKS0
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