5 months ago by
The arrays you are trying to analyze are some old school Mouse 430_2 arrays. These arrays were based on an IVT procedure that uses oligo-dT as the primer, so by definition you are querying only the 3' region of the transcript (e.g. oligo-dT binds to the poly-A tail of the mature transcript, so you start the IVT at the very start of the transcript, and it generally proceeds only so far). More modern Affy arrays use a random primer, so you get cDNA from across the transcript rather than just at the 3' end.
With the more modern arrays (the Gene ST and Exon ST arrays that are being described in that workflow), the probes are dispersed across the entire transcript, so you can summarize subsets of the probes to get measures for individual exons, or you can summarize all of the probes for a given transcript to get a transcript-level measurement. But this isn't possible with the 3'-biased arrays like the Mouse 430_2 arrays you are working with. For those arrays there is only one level at which you can summarize, so there is no 'target' argument to specify different summarization levels.
Another difference has to do with what annotation data are encapsulated in the pdInfoPackage. For the Gene and Exon ST arrays, there are a couple of annotation files that are part of the pdInfoPackage, and you can use
getNetAffx to parse those files. This isn't true of the older arrays. I have a convenience method in my
affycoretools package that is intended to automatically annotate your
ExpressionSet that you can use. For your arrays you would have to install both the
mouse4302.db packages, and then you can do
genePS <- annotateEset(genePS, mouse4302.db)