[BioC] Probe indices for the Drosophila2 Affy chip

[eblanc@ebi.ac.uk]

Thank you for your answer.

nrow( abatch ) returns 732 (as expected), but
getOption("BioC")$affy$xy.offset returns 1 (instead of 0).

Loaded libraries: affy version 1.4.32 and drosophila2cdf version 1.4.7 (in
this order)

Thanks again,
Eric

> Eric Blanc wrote:
>> Dear List,
>>
>> I have problems understanding probe indices for the Drosophila2 chip:
>> the xy2indices and xy2i functions return different values, and I
>> couldn't find anywhere whether either of them has been deprecated. xy2i
>> seems to return indices compatible with pmindex, mmindex and probeIndex
>> functions. (I made sure that the indices from the functions pmindex,
>> mmindex and indexProbes were self-consistent and they are. The MM index
>> always is 732 greater than its corresponding PM index).
>>
>> Also, the number of indices returned by the pmindex, mmindex and
>> probeIndex functions is 42 less than the number of probes in the
>> drosophila2probe data frame. All probes from sets "AFFX-Dm-pd2EGFP_at",
>> "AFFX-Dm-pAsRed2_at" and "AFFX-Dm-pDsRed-Exp_s_at" seem to be missing.
>> I don't know why they don't come up, as they aren't those which have an
>> even y coordinate (only 180 probes in 9 probesets or 20 probes each).
>>
>> So my questions are:
>>
>> 1) Can you confirm that xy2i and i2xy are indeed the functions to use
>> instead of xy2indices and indices2xy ?
>
> These two functions should return the same thing. What do you get from
> nrow(abatch), where abatch is the name of your AffyBatch? Also, what do
> you get from getOption("BioC")$affy$xy.offset?
>
> For the first, you should get 732, and from the second you should get 0.
> If so, the functions should return identical results.
>
>
>> 2) Is there anything wrong with the 3 missing probe sets that I should
>> know ?
>
> I don't think there is anything wrong with them - for whatever reason,
> Affy did not include these three probes in the cdf for this chip, but
> they did include them in the probe_fasta file, which is why you are
> getting differences between the cdfenv and the probe package.
>
> Best,
>
> Jim
>
>
>>
>>
>> platform powerpc-apple-darwin7.4.0
>> arch     powerpc
>> os       darwin7.4.0
>> system   powerpc, darwin7.4.0
>> status
>> major    1
>> minor    9.1
>> year     2004
>> month    06
>> day      21
>> language R
>>
>> affy version 1.4.32
>>
>>
>> Thanks very much for your help,
>> Eric
>>
>> --
>> Dr. Eric Blanc						e-mail: eblanc at ebi.ac.uk
>> European Bioinformatics Institute		Tel: +44 +1223 492 537
>> Wellcome Trust Genome Campus			Fax: +44 +1223 494 468
>> Hinxton - Cambridge CB10 1SD
>> - UNITED KINGDOM -
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> --
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>

--
Dr. Eric Blanc						e-mail: eblanc at ebi.ac.uk
European Bioinformatics Institute		Tel: +44 +1223 492 537
Wellcome Trust Genome Campus			Fax: +44 +1223 494 468
Hinxton - Cambridge CB10 1SD
- UNITED KINGDOM -