Question: Why shouldn't you ever compare TPM values across samples?
gravatar for razbarz
10 weeks ago by
razbarz0 wrote:

There is a warning in red letters in galaxy manual:

"You should NEVER EVER use RPKM, FPKM, or TPM to compare expression levels across samples. These are RELATIVE measures! Consider yourself warned!"

Why? If I want to compare gene X between samples, and TPM normalizes to total reads, shouldn't it be ok to say gene X increase between samples 1 and 2? If someone can direct me to a clear explanation that would be very appreciated


tpm • 214 views
ADD COMMENTlink modified 9 weeks ago by Jennifer Hillman Jackson25k • written 10 weeks ago by razbarz0
gravatar for Jennifer Hillman Jackson
9 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


Using count data directly is more scientifically accurate. Comparing statistics based on a single sample won't result in useful comparison results between samples.

There is much discussion online about this, please review:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 weeks ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour