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Log transformation of RPKM data for PCA analysis

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

rna-seq rpkm pca log-transformation
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updated by Ram Ram • written by AB AB

1 answer

You can just add a value such as 0.01 to all RPKM values for this situations. We routinely add 1 to the raw count value in our analysis.

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updated by Ram Ram • written by Tky Tky

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

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updated by Ram Ram • written by Ashutosh Pandey Ashutosh Pandey

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

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updated by Ram Ram • written by Tky Tky

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