Dear list,

I would appreciate if someone can clarify for me this - seemingly - simple issue:

I have probes for the probe set:
probes1 <- subset(drosophila2probe, Probe.Set.Name == "1631333_s_at")
> as.data.frame(probes1)
                        sequence   x   y Probe.Set.Name Probe.Interrogation.Position Target.Strandedness
119715 CTCACATTCTTCTCCTAATACGATA   2 273   1631333_s_at                         1011           Antisense
119716 CGGCCATTCTGGACTTCTGGGACAA   4 289   1631333_s_at                          490           Antisense
119717 GGTCCCGGTGGTATCATCTGCAACA 564 535   1631333_s_at                          525           Antisense
119718 ATCTGCAACATTGGATCCGTCACTG 656  39   1631333_s_at                          540           Antisense
119719 GGATTCAATGCCATCTACCAGGTGC 467 543   1631333_s_at                          564           Antisense
119720 CGGCGTGACGGCTTACACTGTGAAC  40 289   1631333_s_at                          659           Antisense
119721 TGGTGCACACGTTCAACTCCTGGTT 682 591   1631333_s_at                          706           Antisense
119722 ACTCCTGGTTGGATGTTGAGCCTCA 573 145   1631333_s_at                          721           Antisense
119723 TTGAGCCTCAGGTTGCCGAGAAGCT  93 725   1631333_s_at                          736           Antisense
119724 GAACTTCGTCAAGGCTATCGAGCTG 670 383   1631333_s_at                          800           Antisense
119725 GGAAACTGGACTTGGGCACCCTGGA 399 559   1631333_s_at                          844           Antisense
119726 TGGAGGCCATCCAGTGGACCAAGCA 249 589   1631333_s_at                          865           Antisense
119727 CTGGGACTCCGGCATCTAAGAAGTG 311 285   1631333_s_at                          890           Antisense
119728 AAGGCTGATTCGATGCACACTCACA 612 225   1631333_s_at                          992           Antisense

on the other hand, if
>dat<-ReadAffy()
>y=log2(pm(dat),geneNames(dat)))
>ind<-grep("^1631333_s_at",rownames(y))
>sub<-y[ind,]
> sub
               E1E1_DrosophilaGenome2.0.CEL
1631333_s_at1                          14.11578
1631333_s_at2                          14.22671
1631333_s_at3                          14.16891
1631333_s_at4                          13.29505
1631333_s_at5                          14.28973
1631333_s_at6                          13.73725
1631333_s_at7                          14.33371
1631333_s_at8                          14.15979
1631333_s_at9                          14.30442
1631333_s_at10                         14.70169
1631333_s_at11                         14.25695
1631333_s_at12                         14.39359
1631333_s_at13                         14.51533
1631333_s_at14                         13.42114

Where do the probe numbers 1-14 come from?  I would like to be able to relate them to the information in 'probes1'.
For example, that 1631333_s_at1 is actually N1 in probes1, or something like this.
I thought may be the numbering of probes (119715:119728) in probes1 has something to do with the numbering in y, but this is not the case:
> ind
 [1] 118091 118092 118093 118094 118095 118096 118097 118098 118099 118100 118101 118102 118103 118104

Thank you!
best regards
Galina

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