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9.0 years ago

AB
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360

Hi everyone,

I have the RPKM values from my rna-seq dataset and I want to perform PCA on it. Taking log2 of the RPKM data gives infinity because of all the zeros which is not accepted by prcomp. Is there any other way to use the log transformation without removing the zeros?

Thanks in advance

Adding 1 is more suitable as log2 of values less than 1 will give negative values.

Thanks for pointing out this, I thought it is the log ratio between the two conditions. Adding 1 make sense.