[BioC] getting the pm and mm indices

[James W. MacDonald]

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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-- 
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