[BioC] error with results.summary in simpleaffy

[Jack Zhu]

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