Question: Bioconductor Packages: Transcript Cluster Vs Probeset
3
gravatar for Mike Dewar
8.1 years ago by
Mike Dewar1.5k
Columbia University, NYC, USA
Mike Dewar1.5k wrote:

Hello,

Was wondering if anyone understood the difference between the packages mogene10sttranscriptcluster and mogene10stprobeset? It turns out that I can use the probeIDs that I have (that look like 10345550) with the transcript cluster package, but not the probe set package.

While I can blindly plod on with my analysis, it would be nice to know why one works but the other doesn't! Affy's help pages seem to imply that they're the same thing...

R bioconductor • 2.6k views
ADD COMMENTlink modified 8.1 years ago by Daniel Swan13k • written 8.1 years ago by Mike Dewar1.5k
2
gravatar for Daniel Swan
8.1 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

I think you will find with the exon arrays that the data generated from probe (oligo) signals is summarised into probeset signals to provide a measure of expression of individual exons, the mapping of which is handled by the mogene10stprobeset.db package.

These probesets in turn can be assembled into virtual transcript clusters based on annotations of gene structure and is handled by the mogene10sttranscriptcluster.db package.

A good paper on their use in spotting differential splicing with BioConductor and Limma is here: http://www.biomedcentral.com/1471-2105/10/26

ADD COMMENTlink written 8.1 years ago by Daniel Swan13k
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