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HKS
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@hks-19681
Last seen 5.4 years ago
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?
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..
You can try to work it out yourself. This is out of scope of tximport.
yes, I solved it, Thank you..