[BioC] KEGG2heatmap - blank rows

Lavinia Gordon lavinia.gordon at mcri.edu.au
Thu Oct 15 07:59:33 CEST 2009

   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
   From the help example:
   KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")
   if I do
   foo <- KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")
   > foo
    [1]  2  9  4  6  7  8  3  5  1 10
    [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
   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)
   attached base packages:
   [1] grid      stats     graphics  grDevices utils     datasets  methods
   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

   Lavinia Gordon
   Research Officer
   Murdoch Childrens Research Institute
   Royal Children's Hospital
   Flemington Road Parkville Victoria 3052 Australia
   telephone: +61 3 8341 6221
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