Finding differentially expressed probesets from a single microarray experiment.

Question

[siddharth.avadhanam]

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 :)

[Sean Davis]

What is the platform for the sample?

[siddharth.avadhanam]

Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

[Sean Davis]

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

[siddharth.avadhanam]

yes. I've got the .CEL files

[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?

[siddharth.avadhanam]

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.

Answer 1

[Sean Davis]

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

• http://nar.oxfordjournals.org/content/42/D1/D938.full
• http://barcode.luhs.org/