Hi all,
I would like to use the xps package dabg.call function on MoGene 2.0 st arrays. If I understand correctly on these arrays I have to determine the "exonlevel".
The manual offers the following: "Following exonlevel annotations are valid for whole genome arrays: core: probesets with category ’unique’ and ’mixed’. metacore: probesets with category ’unique’ only. affx: standard AFFX controls. all: combination of above.
Exon levels can also be combined, with following combinations being most useful: exonlevel="metacore+affx": core meta-probesets plus AFFX controls exonlevel="core+extended": probesets with cDNA support exonlevel="core+extended+full": supported plus predicted probesets"
Can you explain what does this mean and which one should I use? I want to use transcript level summarization (option = "transcript"), would it mean I should use the exonlevel="core"?
Thank you in advance! Sophie
