Hi, im working on Exon arrays i.e.. [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version] - GPL5175. I did RMA with target="core" option using oligo package. i got 22011 probe clusters, which im trying to annotate. Is the procedure correct for normalization ? Which package should i use to annotate this data ? Thanks in advance.
target="core" summarises the expression values into transcript (i.e. gene)-level values; whereas,
target="probeset" will leave the expression values at the level of probe-sets. One or may probe-sets may target an individual exon, for example.
For annotation, I do not recommend any package. I recommend that you do a manual curation by obtaining the data straight from the source:
- Go here
- Under section Current NetAffx Annotation Files, download the file HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 36 (79 MB, 7/6/16)
- Unzip the archive, look over the file (even in Excel) and get a feeling of what's in it (it is very comprehensive)
- Do the manual annotation within R by reading in the annotation and matching your transcript IDs to the IDs in the annotation
Not everything should be automated, of course, and annotation packages can be a particular nuisance.
If it helps, I have put some code specifically for this here in an un-responded old thread on Biostars: HuGene-1_1-st accessory files for microarray analysis