Question: Log transformation of RPKM data for PCA analysis
0
gravatar for Apoorva
5.0 years ago by
Apoorva260
United States
Apoorva260 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 2.6 years ago by Biostar ♦♦ 20 • written 5.0 years ago by Apoorva260
2
gravatar for Tky
5.0 years ago by
Tky1000
Japan
Tky1000 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 11 months ago by RamRS30k • written 5.0 years ago by Tky1000
4

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

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.0 years ago by Ashutosh Pandey12k

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

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.0 years ago by Tky1000
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