Question: How to convert Xena Browser normalized RSEM values to TPM values?
gravatar for carlee.bettler
13 months ago by
carlee.bettler10 wrote:

When using the UCSC Xena Browser for gene expression (rna-seq) analysis, it shows the gene-level transcription estimates as a log2(x+1) transformed RSEM normalized count.

Is there a way to convert these values into TPM values? What exactly are the units of these RSEM values?

rna-seq tpm xenabrowser • 755 views
ADD COMMENTlink modified 13 months ago by Charles Warden7.8k • written 13 months ago by carlee.bettler10
gravatar for Charles Warden
13 months ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

I'm not sure if this exactly answers your question, but:

1) Some conversions between expression measurements distributing multi-mapped reads should be possible, but I would have to double-check exactly what was provided to see if I could answer your question about the TPM conversion.

Also, in Xena, I believe you usually search by gene symbol (not transcript ID). So, I'm guessing transcript counts have already been summed by gene symbol (or multi-mapped reads were estimated between genes, rather than among transcripts for the same gene?).

2) The UCSC Xena browser actually provides two different expression measurements, but it is not possible to convert between them (one uses RSEM with multi-mapped read distribution, the other uses htseq-count for only unique reads). However, if you want to get some sense of robustness in your results, you can test both sets of results (with and without "GDC" in the name).

ADD COMMENTlink written 13 months ago by Charles Warden7.8k

Thank you for your response!

ADD REPLYlink written 11 months ago by carlee.bettler10
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