Are these samples good enough for DEA analysis?
0
0
Entering edit mode
6 weeks ago

Hi all, Are these samples good enough for DEA analysis? Because I think the tumor and normal samples are not well separated.

enter image description here Here is my code:

NormalizedCounts.scaled <- t(scale(t(NormalizedCounts) , scale = F))
pc <- prcomp(NormalizedCounts.scaled)

pcr <- data.frame(pc$rotation[,1:3] , Group = gr) 
ggplot(pcr, aes(PC1 , PC2 , color = Group)) + geom_point()

Thanks for any help.

PCA RNA-Seq • 202 views
ADD COMMENT
2
Entering edit mode

This is an awesome separation for clinical data, you will often just see a mess of points with no separation at all because of all the potential confounders in human specimen that obscure the actual clinical effect you're after. Go ahead, plug into your favourit DE software and see what comes out.

ADD REPLY
0
Entering edit mode

Thanks for your positive feedback.

ADD REPLY

Login before adding your answer.

Traffic: 1934 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6