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

[James W. MacDonald]

Dmitry wrote:
> 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)

OK, then how about

gn <- geneNames(Data)
PM <- pm(data, genenames = gn)
MM <- mm(data, genenames = gn)
Cb <- cbind(PM,MM)

Jim

> 
> 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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> 
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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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