Hi, all lists,


I want to use paCalls to filter oligo eset from MoEx-1_0-st-v1 preprocessed by rma. I can use these two functions to filter the data at probe set level as below,
> eset<-rma(OligoRawData,target='probeset')
> dagbPS <- paCalls(OligoRawData, "PSDABG")
> expr_rm_absent<-exprs(eset)[rowSums(dagbPS < 0.05) > N, ]
But someones said that they wouldn't use rma(target = "probeset") for the Gene ST arrays, because tons of the probesets only have one probe at that summarization level. And the only other way to use psCalls with parameter "DABG" for oligo data at probe level. So my question is how to generate probe level eset by rma, or is there some other ways to make paCalls and rma cooperate with each other to process data at "non-probe set" level? In other words, if rma(target = "core") is used, how to use paCalls, and if paCalls("DABG") is used, how to use rma to cooperate with it?


In addition, how to determine the proper value of N in the third commands listed above (expr_rm_absent<-exprs(eset)[rowSums(dagbPS < 0.05) > N, ]), and why?
Looking forward to your reply.


Many thanks in advance.


Best regards.


Chao


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