Search
Question: cummeRbund sigMatrix wrong counts
0
gravatar for Till
23 months ago by
Till0
Till0 wrote:

Hi,

I'm using cummRbund to analyze some data. However the sigMatrix function seems to produce a graph with incorrect counts of DEGs, in my case they are much higher than they should be (as reported by getSig with same alpha).This is the same error as already reported at Seqanswers (http://seqanswers.com/forums/showthread.php?t=51230) it seems.

Is that actually a bug or am I missing something?

Cheers

 

ADD COMMENTlink modified 15 months ago by r.chereji0 • written 23 months ago by Till0
0
gravatar for r.chereji
15 months ago by
r.chereji0
United States
r.chereji0 wrote:

I noticed the same problem: the number of DEGs reported by sigMatrix is higher than the numbers reported by getSig using the same alpha. I would appreciate if someone could clarify why these 2 functions report different numbers and how one could use these 2 functions to get identical results.

Here is a short example:

library(cummeRbund)
cuff = readCufflinks(dir=system.file("extdata", package="cummeRbund"))

mySigMat = sigMatrix(cuff,level='genes',alpha=0.05)
mySigMat

setOfGenes = getSig(cuff,x='iPS',y='hESC',alpha=0.05,level='genes')
length(setOfGenes)

In the previous example, sigMatrix reports 120 DEGs when comparing hESC vs iPS, while getSig reports 117 DEGs. Why are these numbers different? 

 

Thanks!

ADD COMMENTlink modified 15 months ago • written 15 months ago by r.chereji0
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 2.2.0
Traffic: 159 users visited in the last hour