[BioC] Probe indices for the Drosophila2 Affy chip

[James W. MacDonald]

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 -
> 
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-- 
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