Hi

I'm currently running R version 2.2.0 under Windows XP with 2 Gb RAM.

I'm working through the GOstats vignette using the GOstats.Rnw file to 
obtain the R code (for a description of the package see at end of this 
E-mail)

The first objective of this section of the vignette is to extract all of 
the probe sets in the hgu95av2 chip that are associated with 
transcription factor GO identifiers using:

TF2 <- get("GO:0003700", hgu95av2GO2ALLPROBES)

FYI- length(TF2) = 834

The next step gets the locus links (Entrez Gene IDs) associated with 
these probe sets thus:

LLs <- getLL(TF2, "hgu95av2")

FYI - length(LLs) = 834

The third step gets a vector of probe sets that have been selected that 
show some level of expression and some variation in expression across 
samples.  The data is contained within the exprSet = esetSub.

gN = geneNames(esetSub)

FYI - length(gN) = 2391

So far so good.  The next objective is to get probe sets that are common 
to both TF2 and gN and uses the following code:

hv <- match(gN, TF2, 0)

hv contains 159 non zero terms
 > length(hv[!(hv ==0 )])
[1] 159

HOWEVER, THESE NON ZERO TERMS ARE THE INDEX VALUES THAT LOCATE THE PROBE 
SETS in TF2 - NOT in gN!!!  The next part of the code is where the error 
occurs and this error is propagated in the subsequent code for this section.

oTF2 <- gN[hv]

As one would expect from the above, the length(oTF2) does equal 159.  
However, VERY FEW of these probe sets in oTF2 belong to the vector of 
probes selected on the basis of an association with GO::0003700 - that 
is - very few of them (only 14) are actually part of TF2.  Thus:

 > length(oTF2[oTF2 %in% TF2])
[1] 14

whereas all values of oTF2 should be in TF2.

If one revises the above code thus:

hvcorr <- hv[!(hv==0)]

oTF2corr<- TF2[hvcorr]

One again gets length(oTF2corr) = 159 but now the probe sets are in both 
TF2 and gN:

 > length(TF2[TF2 %in% oTF2corr])
[1] 159

 > length(gN[gN %in% oTF2corr])
[1] 159

Thus, all subsequent calculations in this section of the vignette that 
depend on oTF2 are in error.

This problem has probably been raised before and I just now 
rediscovering it.  If so, I would appreciate your pointing me to the 
thread or location of the correction.

Thanks

Carl Garrett




======================================================================
Description
Package: GOstats
Title: Tools for manipulating GO and microarrays.
Version: 1.4.0
Date: 20 Jan 2005
Author: R. Gentleman
Description: A set of tools for interacting with GO and microarray
        data. A variety of basic manipulation tools for graphs,
        hypothesis testing and other simple calculations.
biocViews: Statistics, Annotation, GO, MultipleComparisons
Depends: graph, GO, annotate, RBGL, xtable, Biobase, genefilter,
        multtest
Suggests: hgu95av2 (>= 1.6.0)
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
License: GPL2.0
Packaged: Wed Oct 12 21:34:06 2005; biocbuild
Built: R 2.2.0; ; 2005-10-12 21:34:10; windows



	[[alternative HTML version deleted]]

