[BioC] RMA of CEL files from different chip types

[James W. MacDonald]

Hi Abhishek,

Abhishek Tripathi wrote:
>  Hi All,
> 
>  I have 5 CEL files from HGU133A and 5 from HGU133plus2.
>  The first chip type has 22283 genes and the other has
>  54675 genes.
> 
>  I want to do RMA for all 10 files together taking only
>  22283 common genes from both chip types.
> 
>  How can I do it??

I don't think you can. Well, not easily at least. The coordinates for 
the probes in a given probeset will be different for the two chips, so 
you won't be able to process them together using say, a modified cdf 
package and the rma() function.

Theoretically, you could normalize and background correct the data, then 
extract the PM probe values for each probeset, put these data (on a 
probeset by probeset basis) in a matrix and run medianpolish(). However, 
this would be painfully time consuming. Not to mention any likely 
problems due batch effects.

You would probably be better off processing each chip type separately 
and then trying to combine the data post-processing.

And if you are trying to do a direct comparison of the 133a data to the 
plus2 data (e.g., detect differences between the 133a data and the plus2 
data), then you might as well give up now, as any Biological differences 
will be aliased with batch/chip/time/processing differences.

Best,

Jim


> 
>  I would be thankful for your help.
> 
> Regards,
> Abhishek Tripathi
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623