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Calculation of fpkm

Is it possible to calculate fpkm if only log2 fold change and p-values are provided?

p-values fpkm fold log2 change
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updated by Michael Dondrup Michael Dondrup • written by tthung • tthung

1 answer

I think not. The explanation is simple, disregarding some additional magic to the log fold change like shrinkage, a fold change is essentially a fraction. Say you are given the following information: x/y = 2, what are x and y? Ofc we can't tell, the p-value doesn't help here either.

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written by Michael Dondrup Michael Dondrup

Oh I see. Then I would like to ask how to find the top 100 unregulated genes in R programming ? Cause I would like only calculate the fpkm of a particular genes which is within the top 100 unregulated genes. By finding the top 100 unregulated genes, I can calculate the total number of mapped reads. Then I could calculate fpkm.

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written by tthung • tthung

Just to make sure I understand, "unregulated", as in not differentially expressed? Or up-regulated?

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written by Michael Dondrup Michael Dondrup

oh it's upregulated sorry for the spelling error

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written by tthung • tthung

If you got logFC and p-values (are these adjusted p-values?) you have everything you need. Simply sort all significant genes by logFC (descending or ascending) and pick the top 100. If you could find the original data, that would really help in case you want to do anything more with the data, like plots, clustering, etc.

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written by Michael Dondrup Michael Dondrup

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