[BioC] KEGG2heatmap - blank rows
Saroj K Mohapatra
saroj at vt.edu
Thu Oct 15 10:15:39 CEST 2009
Hi Lavinia:
Lavinia Gordon wrote:
> foo <- KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")
> > foo
> $rowInd
> [1] 2 9 4 6 7 8 3 5 1 10
>
This is in keeping with the fact that there are 10 common probe sets
between the pathway selected and the sample data you used in this example.
> probeids=get("04810", hgu95av2PATH2PROBE)
> intersect(probeids,featureNames(sample.ExpressionSet))
[1] "AFFX-HSAC07/X00351_3_at" "AFFX-HSAC07/X00351_3_st"
[3] "AFFX-HSAC07/X00351_5_at" "AFFX-HSAC07/X00351_5_st"
[5] "AFFX-HSAC07/X00351_M_at" "AFFX-HSAC07/X00351_M_st"
[7] "31719_at" "31720_s_at"
[9] "31699_at" "31557_at"
> $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.
>
It refers to the index of the probe set id (among the 10) after
reordering. On the heatmap, if you start from the bottom, the first
probe set is "AFFX-HSAC07/X00351_3_st", which is the second one on the
list of 10 that I showed above. The second probe set on the heatmap is
"31699_at", which is the 9th one on the list, and so on.
Hope that helps.
Saroj
> 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;LC_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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