Entering edit mode
Nick Henriquez
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20
@nick-henriquez-2869
Last seen 10.2 years ago
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@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_IDENTIFI
CATION
=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
############################