I'm analysing a Rat Gene ST 2.1 array. I would like to filter the dataset using thresholds of expression for a minimum proportion of samples in each group.
I've been following the paper by Rodrigo-Domingo et al. (2014) Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor.
They have two steps to the filtering step, first they filter probesets and then the transcripts. I'm getting stuck at the filtering step (code chunk number 7: intensityFiltering in the R code provided in this paper), as I can't find a way to summarise the Gene St array at the probeset level in order to do the first step. I have used plm <- RmaPlm(can) to summarise my data at the transcript level, but the plmPs <- RmaPlm(csN, mergeGroups = FALSE) seems to summarise by transcripts as well.
So my questions are:
1) Is it possible to summarise a Gene ST array at the probeset level? If yes, how?
2) Less specific to the aroma-affymetrix package, but is it necessary to have the probeset-level dataset in order to filter present/absent probes/transcripts? What would be an appropriate workflow for this?
Thank you very much for your help,
Here is the code chunk from that paper:
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