[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

References

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