Question: Best way to calculate p-value for protein regulations
0
gravatar for alex
4.9 years ago by
alex0
Germany
alex0 wrote:

Hey,

I'm currently working on label-free protein quantification from LC-MS data.

Does anyone of you guys know how to calculate p-values for protein regualtions?

Right now Im using a(n unpaired) t-Test, where the input is simply all measured peptide intensities.

Vulcano plots look quite nice but currently we are understimating the significance of regulations.

I'm sure there are more sofisticated ways how to do it.

Many thanks!

ADD COMMENTlink modified 4.9 years ago by Laurent1.6k • written 4.9 years ago by alex0
2
gravatar for Laurent
4.9 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

You can use the standard tests for your proteomics data - classical t-test, limma, ... and then adjust the p-values. The biggest offender with label-free MS1-level (area under the curve) proteomics will be the missing values. 

Update: you might also look at the Bioconductor package MSstats for dedicated statistical infrastructure. 

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Laurent1.6k

Missing values are not a problem, we have implemented a way to use artifical values in this case which provide a background intensity value.

Since these intensities are very low, i assume this is somewhat problematically for calculating p-values.

ADD REPLYlink written 4.9 years ago by alex0

Missing value imputation is a concern in general. In your case, I would check that the distribution of the values after imputation is still compatible with the assumptions of the test.  

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Laurent1.6k

Is it valid to calculate a paired test on matching peptides?

ADD REPLYlink written 4.9 years ago by alex0

It is difficult to answer that question without information about your experimental design, but I would say no. You would use a paired test when each replicate i of condition C1 matches replicate i of condition C2 - same samples at different time points, or same individuals before/after drug administration. You will always want to compare matching peptides (if that's what you are applying you test on) whether you use a paired test or not. 

ADD REPLYlink written 4.9 years ago by Laurent1.6k
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