[BioC] LIMMA on RT-PCR data

MSU_JPS steibelj at msu.edu
Tue Nov 12 13:48:22 CET 2013

Hello Sandhya
This can be dealt with using a linear mixed effects model that can easily accommodate missing values and the pairing structure of control and test genes.

When I was doing my PhD I came up with this model to help a collaborator with analysis of unbalanced qPCR data. Unfortunately no bioC tool available. But you can use our program or write your own in R using lmer or any other mixed model engine (regress, etc).

Paper: http://www.ncbi.nlm.nih.gov/pubmed/19422910
Tool and other materials: https://www.msu.edu/~steibelj/JP_files/QPCR.html
Juan P.

On Nov 12, 2013, at 6:16 AM, Sandhya Pemmasani Kiran <sandhya.p at ocimumbio.com> wrote:

> Dear list,
> I have RT-PCR data on 4 genes and 85 samples.
> Can I use 'limma' on this small set of genes.
> I want to use limma rather than usual paired t-test because I have missing values and I don't want to miss the information available on paired samples..
> Please advise.
> Thanks,
> Sandhya
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