[BioC] error with results.summary in simpleaffy

[Crispin Miller]

Hi,
I've added a couple of patches to simpleaffy to handle this issue with
the annotation functions in simpleaffy. Hopefully, they'll be bubbling
through the system at the moment.

Cheers,
Crispin


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Norman
Pavelka
Sent: 08 July 2005 19:27
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] error with results.summary in simpleaffy

Hi all,

I was about to report a similar error I encountered after my recent
upgrade to the new 'hgu133a' package (version 1.8.4), when I saw this
thread.

My experience: After some unexplainable error messages, that were
basically telling me that some of the probe set IDs I had found in my
analysis had no match in the 'hgu133aACCNUM' environment, I checked the
content of the package by typing:

hgu133a()

And got as answer:

Quality control information for  hgu133a Date built: Created: Tue May 17
13:02:12 2005

Number of probes: 22277
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
          hgu133aACCNUM found 22277 of 22277
          hgu133aCHRLOC found 20195 of 22277
          hgu133aCHR found 21283 of 22277 ......

In this way I was able to immediately recognize a wrong number of probe
sets, as 22283 were expected to be represented on this Affy chip. So I
looked for the probe set IDs that were missing (using the 'geneNames'  
of an 'eset' containing unfiltered data from an HG-U133A experiment) by
typing:

setdiff(geneNames(eset),ls(hgu133aACCNUM))

and got:

[1] "AFFX-r2-Hs18SrRNA-3_s_at" "AFFX-r2-Hs18SrRNA-5_at"
[3] "AFFX-r2-Hs18SrRNA-M_x_at" "AFFX-r2-Hs28SrRNA-3_at"
[5] "AFFX-r2-Hs28SrRNA-5_at"   "AFFX-r2-Hs28SrRNA-M_at"

So, the probe set ID 'AFFX-r2-Hs18SrRNA-5_at' (mentioned in the initial
mail by Jack Zhu) came out again, explaining the error message he got.
Hope this can help the great job done by the BioC developers to track
down the possible reasons for these missing probe set IDs from the
latest 'hgu133a' annotation package. Just to know, I was wondering when
the fixed version was scheduled to be released...

Best wishes,
Norman
<SNIP>
 
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