Question: Log transformation of RPKM data for PCA analysis
0
gravatar for ApoorvaB
4.6 years ago by
ApoorvaB240
United States
ApoorvaB240 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 2.2 years ago by Biostar ♦♦ 20 • written 4.6 years ago by ApoorvaB240
2
gravatar for Tky
4.6 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 6 months ago by RamRS27k • written 4.6 years ago by Tky1000
4

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

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.6 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 6 months ago by RamRS27k • written 4.6 years ago by Tky1000
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1035 users visited in the last hour