Illumina HT 12 arrays presence and absence calls

Question

[bio_skm]

I would like to find the distribution of present, marginal and absent calls across the entire array (all genes). I have Illumina HT 12 arrays dataset. Please suggest me packages that I can use to find these. Any suggestions are appreciated.

Answer 1

[andrew.j.skelton73]

I guess you're referencing detection P values from the array. Try the lumi package for reading in, normalising and filtering probes that don't have a low enough detection P value, the default threshold is 0.01 in the detectionCall function.

This is what I'd usually do to filter out probes that don't pass detection thresholds.

exprs_data <- exprs(lumi.Q)
present_count <- detectionCall(lumi.Q)
normalised_data <- exprs_data[present_count > 0, ]