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

P.S. > sessionInfo()
R version 2.1.0, 2005-05-12, powerpc-apple-darwin7.9.0

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"   
"grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
    hgu133a   hgu95av2    GOstats   multtest genefilter   survival      
xtable
    "1.8.4"    "1.8.4"    "1.1.3"    "1.7.1"    "1.6.3"     "2.17"     
"1.2-5"
       RBGL   annotate    Biobase         GO      graph      Ruuid     
cluster
   "1.3.13"   "1.5.16"   "1.5.12"    "1.8.2"    "1.5.9"    "1.5.3"     
"1.9.8"

Norman Pavelka
Department of Biotechnology and Bioscience
University of Milano-Bicocca
Piazza della Scienza, 2
20126 Milan, Italy

Phone: +39 02 6448 3556
Fax: +39 02 6448 3552

On 1 Jul 2005, at 12:00, bioconductor-request@stat.math.ethz.ch wrote:

>
> From: "Crispin Miller" <CMiller@PICR.man.ac.uk>
> Date: 1 July 2005 11:03:25 GMT+02:00
> To: "Jack Zhu" <yz8@georgetown.edu>, <bioconductor@stat.math.ethz.ch>
> Subject: Re: [BioC] error with results.summary in simpleaffy
>
>
> Hi,
>
>  We've looked into the problem - it arises because the raw annotation
> data used to build the annotation files in the "hgu133a" package  
> ommited
> some probesets in the latest build. This was breaking the annotation
> lookup calls in simpleaffy. (The issue was occuring within the
> results.summary() function).I've added a work around to the package to
> deal with this (to the devel and release 1.6 branch) - things should
> propagate through the servers in the next few days.
>
>  Cheers,
>
> Crispin
>
>
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Jack Zhu
> Sent: 27 June 2005 19:13
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] error with results.summary in simpleaffy
>
> Hi all,
>
> I used functions of pairwise.filter and results.summary from simpleaffy
> package to do gene filtering and summarization:
>
>     results <- pairwise.comparison(eset, var1,c(group1,group2), spots =
> data_cel)
>     g_inten7 <-
> pairwise.filter(results,min.exp=1,min.exp.no=0,min.present.no=0,present 
> .
> by.group=F,fc=0,tt=1);#trying
> to keep all genes
>     summary_filtered <- results.summary(g_inten7,"hgu133a")
>
> But, I got following error:
>
>> Getting probe level data...
>     Computing p-values
>     Doing PMA Calls
>     Error: value for 'AFFX-r2-Hs18SrRNA-5_at' not found
>
> When I checked 'AFFX-r2-Hs18SrRNA-5_at' in g_inten7 I did see a value  
> in
> 'AFFX-r2-Hs18SrRNA-5_at'.
>
> I'm not sure if this error is associated with hgu133a and hgu133acdf   
> or
> simpleaffy package.
>
> Your help will be highly appreciated.
>
>
> Jack Zhu, MD, MS
>
> Lombardi Cancer center
> Georgetown University
> 3970 Reservoir Rd, NW, NRB, W405b
> Washington, DC 20057
> Email: yz8@georgetwon.edu
> Tel: (202)-687-7451
> Web: http://clarkelabs.georgetown.edu
>

	[[alternative text/enriched version deleted]]

