Question: Finding differentially expressed probesets from a single microarray experiment.
0
gravatar for siddharth.avadhanam
4.2 years ago by
India
siddharth.avadhanam30 wrote:

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 • 1.4k views
ADD COMMENTlink modified 4.2 years ago by Sean Davis25k • written 4.2 years ago by siddharth.avadhanam30

What is the platform for the sample?  

ADD REPLYlink written 4.2 years ago by Sean Davis25k

Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

 

ADD REPLYlink written 4.2 years ago by siddharth.avadhanam30

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

ADD REPLYlink written 4.2 years ago by Sean Davis25k

yes. I've got the .CEL files

ADD REPLYlink written 4.2 years ago by siddharth.avadhanam30

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

ADD REPLYlink written 4.2 years ago by Sean Davis25k

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. 

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by siddharth.avadhanam30
0
gravatar for Sean Davis
4.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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/

 

ADD COMMENTlink written 4.2 years ago by Sean Davis25k
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