proteomics analysis
0
0
Entering edit mode
Shakiba • 0
@bda0add4
Last seen 2.1 years ago
Canada

Hello. I worked with DESeq2 package for analyzing RNA sequencing results, but now I want to work with proteomics data and do some statistics on it and it is important for me to work with R. But I don't know where should I start and which package is suitable. Thanks.

Proteomics analysis • 2.3k views
ADD COMMENT
0
Entering edit mode

Do you want to perform a differential expression analysis on your proteomics data? If so, an option within the bioconductor framework would be msqrob2 https://www.bioconductor.org/packages/release/bioc/html/msqrob2.html, which is from the group I'm working in.

I'm not a proteomics expert myself, but I have heard of people using limma (voom), which has not been developed specifically for proteomics data but has been extensively used for RNA-seq and microarray data as well. Other bioconductor packages I heard of in this context but never used myself are DEqMS and DEP (the differential testing of the latter builds on limma as well if I remember correctly).

ADD REPLY
1
Entering edit mode

If you want limma (which is fine) then use the ‚traditional‘ limma pipeline, not voom. Voom is for digital sequencing data, not the intensity data returned by mass spec, nor for arrays.

ADD REPLY
0
Entering edit mode

Fair point. I was referring to this discussion Using limma for quantitative proteomics data, where at one point limma voom was suggested for the analysis of "quantitative proteomics data". The discussion is quite lengthy though, and not very well formatted, so I am not entirely sure what the end conclusion was.

ADD REPLY
1
Entering edit mode

I refer to several posts from the limma developer (e.g. voom for spectral counts) and others.

ADD REPLY
0
Entering edit mode

Thanks for the reference!

ADD REPLY

Login before adding your answer.

Traffic: 1069 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