Dear BioC community,
I have a list of probe identifiers extracted from the file Clariom_D_Human-hg38-main-probes-tab.zip (field probe_id), downloaded from thermofisher (Affy microarrays).
I want to exclude that list of probes before normalizing the HTAFeatureSet object with rma function, otherwise there's no other way to remove those probes in the downstream analysis:
raw_data <- read.celfiles(filenames = celfiles) raw_data <- raw_data[!featureNames(raw_data) %in% probes2exclude] norm_data <- rma(raw_data)
However, when normalizing with rma, I get the following error:
Error in exprs(object)[pmi, , drop = FALSE] : subscript out of bounds
Does anybody know how to exclude such probes and normalize the HTAFeatureSet without errors?
Thanks in advance