Question: Filtering probesets for HuEx ST1.0 after probeset normalization
gravatar for GENOMIC_region
10 weeks ago by
GENOMIC_region0 wrote:

Hi all,  

I'm working with exon level microarray analysis. I've two annotation files - probeset and transcripts. I normalize data on two targets - gene and probesets to get estimates at gene level and exon level respectively.   

After filtering genes that aren't in probeset annotation and probesets for which genes aren't available I end up with 17K genes and 580K exon probesets.   

Is there a way I can filter these 580K probesets? How?      

I cannot find any function in oligo to calculate dabg.   

Second, can I only work with probesets that are main? filtering probes in affymetrix data   

I have 228349 probesets that are main.   

I maybe wrong in using correct terminology (exon, exon probsets), please correct and pardon me.   



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