Question: Is It Possible To Find Sample Batch # In Cel Files?
1
gravatar for Brian Tsai
6.7 years ago by
Brian Tsai90
Brian Tsai90 wrote:

Hi,

I've been downloading raw CEL files from the Gene Expression Omnibus (GEO), and have been trying to process them -- i'd like to account for batch effect when computing differential expression, but the authors didn't provide the information explicitly in their annotations. Is this information stored/retrievable through the CEL files through Bioconductor?

affymetrix • 2.8k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 6.7 years ago by Brian Tsai90
1

Could you give us the accession number of the experience you are working on? This information should be present in the annotations and in the data describing the experiment (or in the paper). Your last chance, if the information remains inaccessible, is to write an email to the authors of the experiment. Either way, you won't find this information in the CEL files, for sure.

ADD REPLYlink written 6.7 years ago by Leonor Palmeira3.7k
3
gravatar for okko.clevert
6.7 years ago by
okko.clevert220
okko.clevert220 wrote:

Hi, readout the cel-file header using the function readCelHeader in the affxparser package and take a look at the scan date.

ADD COMMENTlink written 6.7 years ago by okko.clevert220
2
gravatar for Sean Davis
6.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

From Wolfgang Huber on the Bioc email list:

the 'readAffy' function in the 'affy' package automatically populates the 'ScanDate' field in the resulting AffyBatch object, which you can access with syntax like protocolData(a)$ScanDate where I have assumed that 'a' is an AffyBatch.

Besides explicitly providing the batches, one can use the sva bioconductor package to "discover" batch effects in the data, so you should consider looking there, also.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Sean Davis25k
0
gravatar for Irsan
6.7 years ago by
Irsan7.0k
Amsterdam
Irsan7.0k wrote:

If you provide a GEO accession number (like Leonor said) we can look it up for you but as long as you don't I suggest you take a look at the GEOquery package and read the vignette on how to deal with GEO data.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Irsan7.0k
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