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 The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}