[BioC] problem with expresso() in affy package

[James W. MacDonald]

Chunrong Dong wrote:
> Dear there:
> 
> When I reduce probe-level data to expression-level data, I tried
> 
>      exprs_norm <- expresso (cels,
>                  bgcorrect.method="none",
>                  normalize.method="invariantset",
>                  pmcorrect.method="subtractmm",
>                  summary.method="liwong")
> 
> and 
> 
>      exprs_norm <- expresso (cels,
>                  bgcorrect.method="none",
>                  normalize.method="invariantset",
>                  pmcorrect.method="mas",
>                  summary.method="liwong")

If the above function calls are exactly what you did, then you simply 
over-wrote the first results with the second, so there is no way to 
compare at that point.

Regardless, it is highly unlikely that you could get the same results 
with these two calls to expresso(). Using some data I have here (and 
renaming the second variable), I get

 > all.equal(exprs(exprs_norm), exprs(exprs_norm1))
[1] "Mean relative  difference: 0.1777846"

Best,

Jim



> 
> Both gave me exactly the same result. It indicates that the two
> pmcorrect.methods "subtractmm" and "mas" works the same which is not
> reasonable. 
> 
> Could anyone help me with this please?
> 
> Thanks.
> 
> Chunrong
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


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