Question: Further analysis of methylation microarrays data (Illumina - idat) after reading by illuminaio package
0
gravatar for Adam
3.6 years ago by
Adam0
Poland
Adam0 wrote:

Hello.

I'm Adam and I'd like to analyze data from methylation microarrays by Illumina. As far as I know there is specific software (GenomeStudio) which allows to preprocessing raw microarray data, then it can be processed in R by lumi package. Nevertheless I'd like to avoid GenomeStudio preprocessing step and analyze my data only with packages implemented in bioconductor.

The analyze pf Affymetrix datasets (.CEL files) doesn't seem to be quite difficult (may tutorials and lenghty manuals).

In case of illumina there are of course good manuals but only for files firstly preprocessed by GenomeStudio.

Files loaded by lumi(from GenomeStudio) and illuminaio(totally raw data) are visibly different.

So my question is what packages and functions should I use to analyze my data to do normalization, quality control, filtering, testing, clustering and finally visualization and interpretation:

data <- readIDAT(my_data)

Of course I don't look for some step by step tutorials or complete solutions, but I'll be very grateful for some hints and tips or show me where shoild I look.

 

Regards

Adam

 

 

ADD COMMENTlink written 3.6 years ago by Adam0
1

There are various packages available: minfi, RnBeads, ChAMP, you can use anyone of them whichever suits your method of analysis.

ADD REPLYlink written 3.6 years ago by AST50

Thank you!

Now I see that is plenty of tools and GenomeStudio isn't necessary.

I'll try a few packages to my analysis.

And for everyone with simmilar lack of knowledge as me :)

I've found nice article about it:

http://www.nature.com/bjc/journal/v109/n6/full/bjc2013496a.html

Regards

Adam

 

ADD REPLYlink written 3.6 years ago by Adam0
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