based on a ongoing analysis of a microarray dataset, with affymetrix platform HTA 2.0, i would like to ask some very quick and specific questions regarding the first steps of preprocessing/normalization/annotation, as this platform is relatively "more complex" that other arrays. In detail,
Based on a similar post that i have created recently: C: Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotati
1) Regarding the rma normalization with the oligo R package, in the option :
data.norm <- rma(affy.cels, target="core")
Again the option "core", is the more appropriate way to move forward, as i would like to perform downstream DE analysis, and this option contains essentially more "safely annotated genes" with the utilization of trancript clusters?
2) Regarding the annotation process, after normalization, still the following functions would be ok, and except the initial R package pd.hta.2.0 and utilization of the R package affycoretools ??:
# firstly remove the control probes with getMainProbes() # and for a quick annotation process: library(hta20transcriptcluster.db) eset.rma <- annotateEset(data.norm, hta20transcriptcluster.db)
3) Finally, the function paCalls from oligo package, is also plaucible for the HTA.2.0 platform ?
Thank you in advance,