Entering edit mode
Lavinia Gordon
▴
480
@lavinia-gordon-2959
Last seen 10.3 years ago
Dear All
I am using KEGG2heatmap (from the annotate package) with the
Affymetrix
chicken array (chicken.db)
With the resulting heatmap, there are a few probe names that appear
as row
names but without any colour in the heatmap.
(I am using the Accent palette which does not contain white).
I have looked for these probe names and they are in my
ExpressionSet. I
thought I might be able to track down the reason by looking at the
output of
KEGG2heatmap.
From the help example:
library("hgu95av2.db")
data(sample.ExpressionSet)
KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")
if I do
foo <- KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")
> foo
$rowInd
[1] 2 9 4 6 7 8 3 5 1 10
$colInd
[1] 13 24 17 19 10 4 26 6 7 2 16 11 9 23 14 25 12 8 15 22 21
18 20
1 3 5
$Rowv
NULL
$Colv
NULL
What does foo$rowInd refer to? I have checked these indexes in
my
ExpressionSet and in the chip data and none of the returned probe
names
appear on the heatmap.
with regards
Lavinia Gordon.
> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;L
C_MONETAR
Y=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods
base
other attached packages:
[1] KEGG.db_2.2.11 SPIA_1.0.0
RCurl_1.2-0
RColorBrewer_1.0-2 gplots_2.7.1 caTools_1.9
[7] bitops_1.0-4.1 gdata_2.6.1
gtools_2.6.1
annotate_1.22.0 chicken.db_2.2.11 RSQLite_0.7-3
[13] DBI_0.2-4 AnnotationDbi_1.6.1
gcrma_2.16.0
Biostrings_2.12.10 IRanges_1.2.3 affy_1.22.1
[19] Biobase_2.4.1 limma_2.18.3
loaded via a namespace (and not attached):
[1] affyio_1.12.0 preprocessCore_1.6.0
splines_2.9.0
xtable_1.5-5
Lavinia Gordon
Research Officer
Bioinformatics
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road Parkville Victoria 3052 Australia
telephone: +61 3 8341 6221
[1]www.mcri.edu.au
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