Question: Microarray differential gene expression analysis using R
gravatar for aharnishi02
3.5 years ago by
aharnishi0280 wrote:


I am new to R and I am keen on learning how to conduct a microarray analysis using Bioconductor. what is the best resource to learn? It could be a recent tutorial/book/online guide. I am in dire need of a guide to trouble shoot my queries.  I want to be able to perform meta-data analysis.

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ADD COMMENTlink modified 3.5 years ago by venu6.2k • written 3.5 years ago by aharnishi0280


ADD REPLYlink written 3.5 years ago by poisonAlien2.8k
gravatar for venu
3.5 years ago by
venu6.2k wrote:

First of all you need to get familiar with R environment. There are many tutorials out there.  

Bioconductor packages you use for analysis depends on the platform used for the data generation for the best results and sometimes integration of different packages into pipeline is needed. In a simple way, you may need to do Data preprocessing (includes filtering low quality probes), normalization, performing statistical tests to find Differentially expressed genes. You can do other things once you get the gene list within a statistical significance cut-off.

For example read this user guide of limma, a bioconductor package for microarray data analysis, followed by this, how the gene set in your hand is useful further.

ADD COMMENTlink written 3.5 years ago by venu6.2k
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