[BioC] error with results.summary in simpleaffy

[Jack Zhu]

 Hi Crispin,

Thank you for your reply.

    results <- pairwise.comparison(eset, var1,c(group1,group2), spots = 
data_cel)

where:
    var1: column in pData(x)
    c(group1,group2): labels in group

Jack


----- Original Message ----- 
From: "Crispin Miller" <CMiller at PICR.man.ac.uk>
To: "Jack Zhu" <yz8 at georgetown.edu>; <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, June 28, 2005 5:25 AM
Subject: RE: [BioC] error with results.summary in simpleaffy


Hi,
What are var1, group1 and group2 in your example?

Crispin


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

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