Hello all,

I came across an apparent discrepancy in the x,y values in the canineprobe 
package as compared to the caninecdf file (both downloaded from 
Bioconductor with the last 2 months) . For many probesets, the order of the 
probes seems to have shifted. For example, for probeset 1592123_at:


 > pmi <- indexProbes(raw,which="pm",genenames="1592123_at")[[1]]
 > indices2xy(pmi,abatch=raw)
         x   y
  [1,] 565 347
  [2,]   5  41
  [3,] 331 327
  [4,] 521 357
  [5,] 542 363
  [6,] 403 601
  [7,] 314 283
  [8,] 135 665
  [9,]   5 679
[10,]  33 647
[11,] 619 181

Compare this with the linear order of the probes as given by the 
canineprobe package:

 > xylist = as.data.frame(canineprobe)
 > xylist[107231:107241,1:4]
                         sequence   x   y Probe.Set.Name
107231 GAACGCCCAGATGCGTGAAAATGGA 542 363     1592123_at
107232 TGAAAATGGAAGAGGAACTTTGCCG 403 601     1592123_at
107233 CGAAGCTTGCTAACTACCAAAGACA 314 283     1592123_at
107234 TACCAAAGACACTTATTGGCCGCCT 135 665     1592123_at
107235 GAGTCAAAATGAAGTTCCGGAAGAC 565 347     1592123_at
107236 TATCAACGAAACTTAGCTTGCCCAG   5 679     1592123_at
107237 TCAACGAAACTTAGCTTGCCCAGAT  33 647     1592123_at
107238 AACGAAACTTAGCTTGCCCAGATTC 619 181     1592123_at
107239 ATGAAGTTCCGGAAGACAGGGTGCA   5  41     1592123_at
107240 GTTCCGGAAGACAGGGTGCAGTCCC 331 327     1592123_at
107241 GAAGACAGGGTGCAGTCCCTCCCCT 521 357     1592123_at


However, other genes have the same order of their probes:

 > pmi2 <- indexProbes(raw,which="pm",genenames="1582358_s_at")[[1]]
 > indices2xy(pmi2,abatch=raw)
         x   y
  [1,] 721  81
  [2,] 575  41
  [3,] 421 179
  [4,] 188 269
  [5,] 459 647
  [6,] 538 197
  [7,] 217 441
  [8,] 448 121
  [9,]  27  37
[10,] 683 389
[11,] 198 255

 > xylist[507:517,1:4]
                      sequence   x   y Probe.Set.Name
507 AGTATGACAACTCCCTCAAGATTGT 721  81   1582358_s_at
508 ATGACAACTCCCTCAAGATTGTCAG 575  41   1582358_s_at
509 AACTCCCTCAAGATTGTCAGCAATG 421 179   1582358_s_at
510 CTCCCTCAAGATTGTCAGCAATGCC 188 269   1582358_s_at
511 TCAAGATTGTCAGCAATGCCTCCTG 459 647   1582358_s_at
512 AAGATTGTCAGCAATGCCTCCTGCA 538 197   1582358_s_at
513 GATTGTCAGCAATGCCTCCTGCACC 217 441   1582358_s_at
514 ACCACCAACTGCTTGGCTCCTCTAG 448 121   1582358_s_at
515 ATCCATGACCACTTCGGCATCGTGG  27  37   1582358_s_at
516 GACCACTTCGGCATCGTGGAGGGCC 683 389   1582358_s_at
517 CTTCGGCATCGTGGAGGGCCTCATG 198 255   1582358_s_at

The discrepancy seems to be wide-spread. The actual order of the probesets 
themselves is different (1582358_s_at is the first probeset in the 
affybatch, but it starts at row 507 in the xylist from the canineprobe). Is 
it possible that the linear order is not really the probe number order, and 
the actual probe numbers can be gotten for each x,y coordinate? I tried the 
same sorts of things with the rat2302cdf and rat2302probe packages, but 
there are no discrepancies between probe orders, which made me think it was 
a problem with the canineprobe package itself. I'd appreciate any and all 
help on this matter...

Thanks,
Jenny




Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@uiuc.edu 
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