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

[Dmitry]

Thank you,

I tried this. The output is not exactly what I needed: 

1007_s_at	649	371
1007_s_at.1	952	1043
1007_s_at.2	1640	2892
1007_s_at.3	3505	4894
1007_s_at.4	3703	2188
1007_s_at.6	2822	1812

Why should we re-create names for the rows whcih (names) are already there? 
Is there any function which will allow to retrieve the whole line of PM and
MM values for several chips at once, with one row ID?
I used to loop through my:
 
PM<-pm(Data)
MM<-mm(Data)
Cb<-cbind(PM,MM)

and was happy till pm() and mm() stop working:-)

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Thursday, April 06, 2006 2:45 PM
To: Dmitry
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] pm() mm() functionality changed?

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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