Question: fpkm to tpm conversion
0
gravatar for sayamsmruti
4 weeks ago by
sayamsmruti0 wrote:

how to convert the fpkm value generated from cufflink to tpm value using r programming????

next-gen R • 309 views
ADD COMMENTlink modified 29 days ago • written 4 weeks ago by sayamsmruti0

Please, read this article for basic calculation,

http://bioinfogeek.over-blog.com/2017/09/gene-expression-units-explained-rpm-rpkm-fpkm-and-tpm.html

ADD REPLYlink written 4 weeks ago by Renesh1.1k

actually after doing cufflink i got the genes.fpkm_tracking as output file so i am clueless what to do next for further data analysis, and how can i convert the generated fpkm values to tpm values...plzz can sum1 help out

ADD REPLYlink written 29 days ago by sayamsmruti0
1

Hi, I highly recommend to leave the cufflinks fpkm output alone and use a more simple and state-of-the-art approach such as featureCounts or HTseq-count directly from BAM files and then generate TPM or CPM from the counts directly using RSEM. In addition I recommend to provide more information, your question is pretty unspecific, and please avoid chat jargon like "plzz sum1". The R-programming portion should be ignored unless there are multiple alternative ways to do this.

ADD REPLYlink modified 29 days ago • written 29 days ago by Michael Dondrup43k
2
gravatar for Satyajeet Khare
4 weeks ago by
Satyajeet Khare1.1k
Pune, India
Satyajeet Khare1.1k wrote:

It is going to be difficult to calculate TPM from FPKM values in Cuffdiff unless you have raw count values or gene length vector. I would suggest moving to count based methods since the old Tuxedo protocol is deprecated.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Satyajeet Khare1.1k

You can still calculate TPM from RPKM/FPKM values.You need to have information about a total number of transcripts sampled from your read data and avg. a number of nucleotides mapped to each gene.

ADD REPLYlink written 4 weeks ago by Renesh1.1k

I think the issue is RPKM to TPM conversion in cuffdiff. RPKM values in cuffdiff are internally normalized. When calculated from raw counts, it should not be an issue.

Best

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Satyajeet Khare1.1k

no, actually it is the fpkm value generated from cufflink, i am unable to convert the fpkm values to tpm

ADD REPLYlink written 28 days ago by sayamsmruti0
1
gravatar for lucianalpt
4 weeks ago by
lucianalpt20
lucianalpt20 wrote:

Actually, you can convert in R by the function I got from another forum and used.

fpkmToTpm <- function(fpkm) {

exp(log(fpkm) - log(sum(fpkm)) + log(1e6))

}

where fpkm is the values you got from TCGA for example.

Luciana

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by lucianalpt20
1

How do you want to cite that in a paper? In general we do not recommend to convert directly between normalized counts because they could been based on whatever non-linear transformation.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Michael Dondrup43k

For a small dataset (raw counts) I tested, it did work fine. I did not expect the formula to be so simple :). Thanks for this input. Looking forward to learn more from this discussion.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Satyajeet Khare1.1k
1
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