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 > 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 > > 1. [1]http://www.mcri.edu.au/ > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > [2]https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: [3]http://news.gmane.org/gmane.science.biology.informatics.conductor > > ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch [4]https://stat.ethz.ch/mailman/listinfo/bioconductor 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 1. http://www.mcri.edu.au/ 2. https://stat.ethz.ch/mailman/listinfo/bioconductor 3. http://news.gmane.org/gmane.science.biology.informatics.conductor 4. https://stat.ethz.ch/mailman/listinfo/bioconductor 5. http://www.mcri.edu.au/