[BioC] pm() mm() functionality changed?

[James W. MacDonald]

Dmitry wrote:
> Hi ALL,
> 
> What happened to pm() and mm() functions?
> I'm running my old scripts:
>  
> PM<-pm(Data)
> MM<-mm(Data)
> Cb<-cbind(PM,MM)
> 
> And my Cb output looks like this:
> 
> 1       378     52
> 2       930     486
> 3       1424    463
> 4       93      47
> 5       248     83
> 6       314     122
> 
> But I need my old way with probe pair ids instead of indices:
> 
> 1007_s_at1	649	371
> 1007_s_at2	952	1043
> 1007_s_at3	1640	2892
> 1007_s_at4	3505	4894
> 1007_s_at5	3703	2188
> 1007_s_at6	2822	1812
> 
> I tried:
>  
> GN<-probeNames(Data)
> PM<-pm(Data)
> MM<-mm(Data)
> Cb<-cbind(GN,PM,MM)

Try

Cb <- data.frame(PM, MM, row.names = make.names(GN, unique = TRUE))

HTH,

Jim

> 
> But the Cb output doesn't identify probe pare numbers
> 
> 1007_s_at	649	371
> 1007_s_at	952	1043
> 1007_s_at	1640	2892
> 1007_s_at	3505	4894
> 1007_s_at	3703	2188
> 1007_s_at	2822	1812
> 
> Of cause I could script for those identifiers but is there a simple way to
> reproduce my old output with this altered pm() and mm()?
> 
> 
> Thank you
> 
> Dmitry
> 
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-- 
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


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