[BioC] getting the pm and mm indices

[Donna Toleno]

Thank you for pointing that out. I'm not sure how I caused that behavior. The important point is that I somehow caused it and it is not a problem with the way the get command works. That's a relief. 

I am still trying to diagnose a problem with some code. I think the nature of the problem is that when I remove all but one probe in a set from the cdf file then I am left with  something that looks something like this:

>      a<-get("1552287_s_at", env=get(cdfpackagename))
> a
    pm     mm 
379214 380378 

So there are no row numbers in this case, and I believe it is affecting my downstream code because the indices are lacking a dimension. 

Like this:

some_pmIndex <-  indexProbes(newAB,which="pm",genenames="1552287_s_at")[[1]]
Error in ans[[i]][, i.probes] : incorrect number of dimensions

I'll do some more testing to confirm the problem.

Any ideas would be appreciated.

Thanks for your patience.

-Donna






----- Original Message -----
From: "James W. MacDonald" <jmacdon at med.umich.edu>
Date: Wednesday, November 21, 2007 9:53 am
Subject: Re: [BioC] getting the pm and mm indices
To: Donna Toleno <toleno at usc.edu>
Cc: bioconductor at stat.math.ethz.ch

> I don't see that:
> 
> > library(hgu133plus2cdf)
> 
> Attaching package: 'hgu133plus2cdf'
> 
> > get("1053_at", hgu133plus2cdf)
>            pm      mm
>  [1,] 1193929 1195093
>  [2,]   48229   49393
>  [3,] 1014367 1015531
>  [4,] 1076821 1077985
>  [5,]  975016  976180
>  [6,]  201506  202670
>  [7,]  895292  896456
>  [8,] 1170808 1171972
>  [9,]   81075   82239
> [10,]  134485  135649
> [11,]  714108  715272
> [12,]  956498  957662
> [13,]  429738  430902
> [14,]   62512   63676
> [15,]  462278  463442
> [16,]  276396  277560
> > get("241053_at", hgu133plus2cdf)
>            pm      mm
>  [1,]  620561  621725
>  [2,] 1151233 1152397
>  [3,]  477004  478168
>  [4,]  742568  743732
>  [5,]  930540  931704
>  [6,]  288662  289826
>  [7,]  255492  256656
>  [8,]  623319  624483
>  [9,] 1172293 1173457
> [10,]   11589   12753
> [11,] 1000379 1001543
> > indexProbes(dat, "pm")["1053_at"]
> $`1053_at`
>  [1] 1193929   48229 1014367 1076821  975016  201506  895292 
> 1170808 
> 81075
> [10]  134485  714108  956498  429738   62512  462278  276396
> > indexProbes(dat, "pm")["241053_at"]
> $`241053_at`
>  [1]  620561 1151233  477004  742568  930540  288662  255492  
> 623319 
> 1172293
> [10]   11589 1000379
> 
> > sessionInfo()
> R version 2.6.0 beta (2007-09-24 r42966)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices datasets  utils     
> methods[8] base
> 
> other attached packages:
> [1] hgu133plus2cdf_1.17.0 affy_1.16.0           preprocessCore_1.0.0
> [4] affyio_1.6.0          Biobase_1.16.0        rcompgen_0.1-15
> 
> Best,
> 
> Jim
> 
> 
> 
> Donna Toleno wrote:
> > Hello Bioconductor list,
> > 
> > I am using the  "hgu133plus2cdf" as my cdfpackagename
> > and I notice that I have a problem with the following commands 
> when a probe name is nested within other probenames. 
> > 
> > There is a probe named   "1053_at"  and   "241053_at"
> > 
> > For example, 
> > 
> >> a <- get("1053_at", env=get(cdfpackagename))
> >> a
> > pm mm 
> > NA NA 
> > 
> > 
> >> indexProbes(mydata, "pm")["1053_at"]
> > $`1053_at`
> > pm mm 
> > NA NA 
> > 
> >> indexProbes(mydata, "pm")["1007_s_at"]
> > $`1007_s_at`
> >  [1]  369707  563318 1049349  238813 1140401 1130782 1144961  
> 207148 1144717  285805 1351879 1170814  906807
> > [14]  547053 1221909   2761
> > 
> > is the getProbeDataAffy a potential solution?
> > 
> > _______________________________________________
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> > Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> -- 
> 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
>