Question: Analysis Of Shotgun Proteomics Data
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gravatar for 9921
6.3 years ago by
99210
99210 wrote:

Hi everyone, I have 3 samples (Cell) with 3 replicate. In shotgun proteomics 1750 protein with variable expression identified for each sample . How can I found up and down regulation protein between 3 samples? How can I do ANOVA analysis for them? Thanks

proteomics • 2.5k views
ADD COMMENTlink modified 6.3 years ago by Michael Dondrup47k • written 6.3 years ago by 99210
1

You say "3 sample (Cell) with 3 replicate", by that do you mean "3 cell-types with 3 biological replicates each"? I assume that's what you mean, but figured I'd ask before incorrectly answering. BTW, you probably just want pairwise t-tests, since I suspect you'll want p-values for each of the 3 comparisons.

ADD REPLYlink written 6.3 years ago by Devon Ryan94k
1

Please be more specific (I think that's the most used request on scientific forums?). It is very hard to answer your question, because we do not know what your problem really is. Also, I find it rude to have two obvious typos in the tags, couldn't you take a little more care if the answer means anything to you?

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Michael Dondrup47k
1
gravatar for Devon Ryan
6.3 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

Given the N of 3 per group, you're likely to want to share information across proteins. In that case, you could actually just use limma in R/Bioconductor. There happens to be a thread on the Bioconductor list discussing analysing proteomics data here. That thread also discusses possible data transformation methods that you might pursue, since you've not otherwise mentioned anything about the form your data takes.

ADD COMMENTlink written 6.3 years ago by Devon Ryan94k
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