How to set the control group in microarray analysis from illumina data?
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5.4 years ago
dodausp ▴ 150

Hi, there

I am sorry for for the sounded simple question, but how do I set up my control group when processing my data to be used for analysis?

Say I have 3 groups in triplicates (all extracted from Genome Studio), being:

control (C1, C2, C3); Treatment A (A1, A2 ,A3); and Treatment B (B1, B2, B3).

Now, I am able to load the files to R (using Beadarray package), together with the control (probes) table - it generates a EListRaw object. I am also able to run the normalization (neqc), fit linear model (lmFit), and empirical Bayes analysis (eBayes) with no problems. And as expected, you have 3 possible contrast analysis in there: C vs A, C vs B and A vs B.

However, here is my question, how do I compare A vs B where both are already normalized to the control, or put it more simple, how do I compare log2(A/C) vs log2(B/C)? Is there any function in R where I can do this?

Please, any help will be much appreciated.

Douglas.

 

illumina R limma beadarray directhyb • 1.6k views
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Entering edit mode
5.4 years ago
vassialk ▴ 200

Use Expander, MeV and Genesis and JMP, Cytoscape softwares then go to R and Python. Writing code is a big skill and science. You are not obliged to do it for your task.

When you say "compare", you perhaps say about running ttest or ANOVA on groups or test like LIMMA.

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