Question: Log transformation of RPKM data for PCA analysis
0
gravatar for ApoorvaB
2.9 years ago by
ApoorvaB140
United States
ApoorvaB140 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 6 months ago by Biostar ♦♦ 20 • written 2.9 years ago by ApoorvaB140
2
gravatar for Tky
2.9 years ago by
Tky980
Japan
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 2.9 years ago • written 2.9 years ago by Tky980
4

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

 

ADD REPLYlink written 2.9 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 2.9 years ago by Tky980
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: 767 users visited in the last hour