[BioC] error with results.summary in simpleaffy

Crispin Miller CMiller at PICR.man.ac.uk
Fri Jul 1 11:03:25 CEST 2005

 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.


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jack Zhu
Sent: 27 June 2005 19:13
To: bioconductor at 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 =
    g_inten7 <-
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

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 at georgetwon.edu
Tel: (202)-687-7451
Web: http://clarkelabs.georgetown.edu

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