Question: lumi: can't see sample corr pairwise and MAplot plots
gravatar for Frederico Moraes Ferreira
3.9 years ago by

Dear List, 

Perhaps this is a stupid question, but I could found an answer to that. I can´ t be able to see the lumi QC sample correlation pairwise and also MAplot plots due to a high number of samples (150). Well, of course I don't intend to see all of the them. However, it would be desirable to check at least a few number of plots. How people have been dealing with such problem? Thanks in advance.


ADD COMMENTlink modified 3.8 years ago by Gordon Smyth35k • written 3.9 years ago by Frederico Moraes Ferreira100
gravatar for Gordon Smyth
3.8 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

Not sure how to solve your problem with the lumi package. An alternative is to read your read your Illumina BeadChip files using the read.ilmn() function of the limma package. Then you can normalize using neqc() and make MA plots one at a time using plotMA().

ADD COMMENTlink written 3.8 years ago by Gordon Smyth35k
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