[BioC] affycoretools vennSelect problem

[Nick Henriquez]

Dear Paedar,

I don't actually know the Vennselect wrapper but I find that when I export
contrasts of Venn diagrams from Limma I always get the FULL diagram (e.g. 1,
0, -1, 0, 1) for each probe set on my chip and in the order of the imported
genelist. I presume this is so I can safely "reattach" the annotations,
expression levels and all sorts of other info which is missing from the
Venntable, and this is precisely what I use it for. Subsequent ordering by
p-value, contrast, contrast combinations, in the spreadsheet program of
choice allows me to follow up on all sorts of subsets. 

So I assume you will find Vennselect provides the full list, just like my
"old" version. If you don't want the rest- you can always delete it ;-)

If you only got the selected genes (some of) the annotation might possibly
still be present, but I certainly don't want to be the one who re-inserts
all the extra information I had before I imported the file into R/BioC. Not
if there are more than a few genes and I tend to get 100s. Also I find it
interesting to see that e.g. geneX only JUST falls out of my cutoff etc.

Best regards,

Nick



------------------------------

Message: 2
Date: Mon, 23 Jun 2008 12:50:19 +0000
From: Peadar ? Gaora <peadar.ogaora at ucd.ie>
Subject: [BioC] affycoretools vennSelect problem
To: bioconductor at stat.math.ethz.ch
Message-ID: <1214225419.25084.111.camel at pogpc.ucd.ie>
Content-Type: text/plain; charset=ISO-8859-15

Hello BioCer's,

I've been using affycoretools, particularly limma2annaffy,for a while
now and love it.  These wrappers really make life simpler.

However (there was bound to be a however), in a recent experiment I've
had some problems with vennSelect.  The experiment has 4 groups and 4
time points, 5 replicates each.  There are then, a plethora of possible
contrasts of interest.  I've run one particular analysis with 34
contrasts and wanted to look at the unique (differentially expressed,
p<0.05) genes and intersections between some of them.  When I use
vennSelect to do this, it returns probesets with P values well above
0.05.

I can't see where it is picking these from as the lists from the
individual contrasts all look perfectly fine (P-value for all selected
genes < 0.05).  I have tried subsetting the TestResults and contrasts
matrices in the call to vennSelect.  I've also tried generating new ones
TestResults objext and contrast matrix which include only the
comparisons being analysed.  The fit object however contains the entire
dataset.  Could this be where things are going wrong?


Any help much appreciated.

Peadar


> sessionInfo()
R version 2.5.1 (2007-06-27)
ia64-unknown-linux-gnu

locale:
LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_IE.UTF-8
;LC_MONETARY=en_IE.UTF-8;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_IE.UTF-8;LC_NAM
E=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDENTIFICATION
=C

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

other attached packages:
affycoretools       annaffy        xtable         gcrma   matchprobes
      "1.8.1"       "1.8.1"       "1.5-1"       "2.8.1"       "1.8.1"
      biomaRt         RCurl           XML       GOstats      Category
     "1.10.1"       "0.8-0"      "1.92-1"       "2.2.6"       "2.2.3"
       Matrix       lattice    genefilter      survival          KEGG
 "0.999375-2"     "0.15-11"      "1.14.1"        "2.32"      "1.16.1"
         RBGL      annotate            GO         graph         limma
     "1.12.0"      "1.14.1"      "1.16.0"      "1.14.2"      "2.10.5"
         affy        affyio       Biobase
     "1.14.2"       "1.4.1"      "1.14.1"

-- 


############################
Dr. Peadar ? Gaora
UCD Conway Institute,
Belfield,
Dublin 4.

(01) 716-6915
############################