Question: Log transformation of RPKM data for PCA analysis
gravatar for AB
2.6 years ago by
United States
AB90 wrote:

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

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 2.6 years ago by AB90
gravatar for Tky
2.6 years ago by
Tky980 wrote:

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.  

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Tky980

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


ADD REPLYlink written 2.6 years ago by Ashutosh Pandey11k

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

ADD REPLYlink written 2.6 years ago by Tky980
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