[BioC] Bioconductor Digest, Vol 80, Issue 15
Lavinia Gordon
lavinia.gordon at mcri.edu.au
Fri Oct 16 02:09:37 CEST 2009
Hi Saroj
Thank you very much for your reply.
I still don't know why some of the KEGG2heatmap appears blank, but using
your suggestions, I can extract the matrix and plot it using heatmap.2,
which looks great.
Many thanks,
Lavinia.
Message: 15
Date: Thu, 15 Oct 2009 13:45:39 +0530
From: Saroj K Mohapatra <saroj at vt.edu>
Subject: Re: [BioC] KEGG2heatmap - blank rows
To: Lavinia Gordon <lavinia.gordon at mcri.edu.au>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <4AD6DA2B.7040207 at vt.edu>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
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_MONET
AR
> 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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End of Bioconductor Digest, Vol 80, Issue 15
********************************************
Lavinia Gordon
Research Officer
Bioinformatics
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road Parkville Victoria 3052 Australia
telephone: +61 3 8341 6221
[5]www.mcri.edu.au
This e-mail and any attachments to it (the "Communication") are, unless
otherwise stated, confidential, may contain copyright material and is for
the use only of the intended recipient. If you receive the Communication in
error, please notify the sender immediately by return e-mail, delete the
Communication and the return e-mail, and do not read, copy, retransmit or
otherwise deal with it. Any views expressed in the Communication are those
of the individual sender only, unless expressly stated to be those of
Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its
related entities. MCRI does not accept liability in connection with the
integrity of or errors in the Communication, computer virus, data
corruption, interference or delay arising from or in respect of the
Communication.
Please consider the environment before printing this email
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