<p>I have raw gene read counts and would like to perform an analysis across multiple samples. I've found conflicting info online on how this should be done. One commonality however is that FPKM/RPKM should not be used. On the other hand, there seems (to me at least) to be conflict about whether TPM is suitable. For example, <a href="https://www.youtube.com/watch?v=TTUrtCY2k-w" rel="nofollow noreferrer">this StatQuest video</a> seems to suggest that TPM is suitable for analysis across samples. One person on <a href="https://www.biostars.org/p/273537/" rel="nofollow noreferrer">this Biostar post</a> (among other resources I've looked at) suggested that none of the units (FPKM, RPKM, TPM) are suitable for cross sample comparisons. 
I am quite confused. Can someone clear up the confusion?</p>

CC BY-SA 4.0
2020-06-07T19:57:58.537Z
Choices in bioinformatics tend to be quite situation dependent; could you please provide more information about the specific problem you're having? What tool are you using for mapping? Are the reads long reads, paired end, or single reads?
gringer
<differential-expression><gene-expression><normalization>
What unit (TPM, FPKM/RPKM, or other) to use when working across samples
# What unit (TPM, FPKM/RPKM, or other) to use when working across samples

(Asked by: username_0 on 2020-06-07)

I have raw gene read counts and would like to perform an analysis across multiple samples. I've found conflicting info online on how this should be done. One commonality however is that FPKM/RPKM should not be used. On the other hand, there seems (to me at least) to be conflict about whether TPM is suitable. For example, [this StatQuest video](https://www.youtube.com/watch?v=TTUrtCY2k-w) seems to suggest that TPM is suitable for analysis across samples. One person on [this Biostar post](https://www.biostars.org/p/273537/) (among other resources I've looked at) suggested that none of the units (FPKM, RPKM, TPM) are suitable for cross sample comparisons.
I am quite confused. Can someone clear up the confusion?

**Tags:** differential-expression, gene-expression, normalization
> **Comments:**
> **username_1**: Choices in bioinformatics tend to be quite situation dependent; could you please provide more information about the specific problem you're having? What tool are you using for mapping? Are the reads long reads, paired end, or single reads?  

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## 0 answers

