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Finding differentially expressed probesets from a single microarray experiment.

Hi

I need to extract expressed gene probe-sets from a microarray control experiment. It is a single GEO dataset, with a single cy3 labelled control sample. I understand that the way to go about this is to set some threshold value (based on the distribution of intensities) and then extract all the probeset ids with values above the threshold value. Any ideas how to go about this ? I would like to implement this in R/Bioconductor, but if there are software packages online that will accomplish this task that would be fine too.

Any help would be much appreciated

Thanks :)

r gene
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updated by Ram Ram • written by siddharth.avadhanam • siddharth.avadhanam

What is the platform for the sample?

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updated by Ram Ram • written by Sean Davis Sean Davis

And are the raw data (the .txt file, for agilent) available?

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updated by Ram Ram • written by Sean Davis Sean Davis

Agilent does not use .CEL format -- could you clarify? Also, I thought you were talking about just a single array. Is that the case?

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updated by Ram Ram • written by Sean Davis Sean Davis

Sorry. This is an Affymetrix dataset. Affymetrix HT HG-U133+ PM Array Plate. And yes, I am referring to a single array. I've got multiple .CEL files as the replicates. But I would like to know how to performed the aforementioned analysis on a single array.

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updated by Ram Ram • written by siddharth.avadhanam • siddharth.avadhanam

1 answer

You might take a look at using the gene expression barcode approach:

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updated by Ram Ram • written by Sean Davis Sean Davis

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