[BioC] extraction of detectable genes in illumina data.

[Zara Ghazoui]

Dear Bioconductor users,

I am writing to ask a small query to do with the retrieval of
detectable genes in illumina data using "Lumi" package.  I have a data
of just over 43000 features and roughly about 26.5% of the genes are
detectable at a detection P value of 1% (according to the QC summary). 
My question is how to retrieve only the detectable genes and still have
them as a lumiBatch object i.e. need to some sort of subset on the
entire data for only the detectable genes (detection P value <= 1%). 

What I have tried is the following:

presentCount <- detectionCall(x.lumi)
median(presentCount) which is equal 0.265
oppDataMatrix <- dataMatrix[presentCount < 0.265, ]

Then I ended up with half of the dataset.  I thought that this dataset
would contain all the genes detected with a P value <=1% but it is not
the case as I seem to be missing some important genes that are detected
with P values << 1%.

Please could you advice as I really need to fix this problem.

Many thanks and best wishes.

Zara

 

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