how to obtain a normalised expression matrix from read counts and scaling factors
I have a read count matrix (row: genes; column: samples) from which I generated scaling factors using EdgeR 'calcNormFactors' function, set with different methods ("TMM","RLE","upperquartile").
Now I have my raw read counts matrix and vectors of scaling factors for each samples.
How do I get a normalised expression matrix:
raw count / scaling factor
OR
raw count * scaling factor
OR
raw count / (library size * scaling factor)
or by another way?
Thanks for your explanations.
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Hello user31888!
Please do not post the same question from multiple accounts. This does not increase your chances of getting an answer. If you edit your post (without changing any content) it gets bumped to main page and will be seen on first page once again. (like posting a new question)
Previous question: Normalization scaling factors: formula for applying them to raw counts
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
Yep I disagree since it was another person asking the question in the thread you mentioned (people still have multiple accounts seriously ???). This same question did not pop up in the search field when I was writing my question. Anyway I got my answer I guess :)
In any case, you have an answer you could use for this question.
Just 2 people trying to ask a basic question about the most used technique nowadays maybe. Anyway you are just doing your job, no worries.