Hi Michael, I can't know very much about what you are doing from your post as you have not given us much code to go on let alone a reproducible example. You might want to peek at the posting guide here: http://www.bioconductor.org/help/mailing-list/posting-guide/ Anyhow, I can tell you one thing that might help: org packages do not contain any information about probe IDs. So if your software is asking about probe IDs, it suggests that something you are using may be expecting a chip package. There are some descriptions about the different types of annotation packages used in Bioconductor on our web site here: http://www.bioconductor.org/help/workflows/annotation-data/ Since you are using ChromHeatMap to try and plot RNA-seq data, I speculate that (at a minimum) you have to make the identifiers for your count data match the primary identifier for the annotation package. In this case, you are using an org package, so that would mean using an entrez gene ID. If you don't do this, you will probably have troubles later on. But I also looked at the source code for makeChrStrandData. And in doing so, I see the code that throws the error you described seems to have almost nothing to do with the kind of annotation that is present. This error will be tripped if there are unlabeled rows in your expression matrix. So you need to make sure that your matrix has names for each row and that they are all Entrez Gene IDs. Marc On 08/19/2010 09:15 AM, Michael Muratet wrote: > Greetings > > I am attempting to make a ChromHeatMap from RNA-seq data with Entrez > IDs using org.Mm.eg for annotation. The original data was aligned to > the UCSC knownGenes table and I can map the original identifiers to > just about any other system using the browser tables. I tried > > > chrData <- makeChrStrandData(matrix(neuro.ca.7d), lib="org.Mm.eg") > Error in makeChrStrandData(matrix(neuro.ca.7d), lib = "org.Mm.eg") : > Error: Data matrix must have row names corresponding to probe IDs. > > I suspect that I'm missing a step somewhere but I can't find it in the > documentation. Is there a way to get the annotation from the org.Mm.eg > data? > > Thanks > > Mike > > Session info: > > R version 2.11.0 (2010-04-22) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] ChromHeatMap_1.2.0 hgu95av2.db_2.4.1 > [3] org.Hs.eg.db_2.4.1 ALL_1.4.7 > [5] org.Mm.eg.db_2.4.1 RSQLite_0.8-4 > [7] DBI_0.2-5 > BSgenome.Mmusculus.UCSC.mm9_1.3.16 > [9] BSgenome_1.16.5 Biostrings_2.16.7 > [11] GenomicRanges_1.0.5 IRanges_1.6.8 > [13] vsn_3.16.0 limma_3.4.4 > [15] gplots_2.7.4 caTools_1.10 > [17] bitops_1.0-4.1 gdata_2.7.1 > [19] gtools_2.6.1 DESeq_1.0.4 > [21] locfit_1.5-6 akima_0.5-4 > [23] geneplotter_1.26.0 lattice_0.18-5 > [25] annotate_1.26.1 AnnotationDbi_1.10.0 > [27] Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affy_1.26.1 affyio_1.16.0 genefilter_1.30.0 > preprocessCore_1.10.0 > [5] RColorBrewer_1.0-2 RCurl_1.3-1 rtracklayer_1.8.1 > splines_2.11.0 > [9] survival_2.35-8 tools_2.11.0 XML_2.8-1 > xtable_1.5-6 > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > mmuratet at hudsonalpha.org > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Mike, Thanks for your email, and thanks to Marc for stepping in so promptly. Marc's analysis is quite correct - the makeChrStrandData function needs the row names of your data matrix to correspond to the probe or gene identifiers used by the annotation library package. In the case of org.Mm.eg.db the row names should correspond to Entrez IDs. The package was originally written for chip-based data but there's no reason it shouldn't also work in your case. I'll update the documentation to make that a bit clearer. Best regards, Tim Rayner On 19 August 2010 17:15, Michael Muratet <mmuratet at="" hudsonalpha.org=""> wrote: > Greetings > > I am attempting to make a ChromHeatMap from RNA-seq data with Entrez IDs > using org.Mm.eg for annotation. The original data was aligned to the UCSC > knownGenes table and I can map the original identifiers to just about any > other system using the browser tables. I tried > >> chrData <- makeChrStrandData(matrix(neuro.ca.7d), lib="org.Mm.eg") > Error in makeChrStrandData(matrix(neuro.ca.7d), lib = "org.Mm.eg") : > ?Error: Data matrix must have row names corresponding to probe IDs. > > I suspect that I'm missing a step somewhere but I can't find it in the > documentation. Is there a way to get the annotation from the org.Mm.eg data? > > Thanks > > Mike > > Session info: > > R version 2.11.0 (2010-04-22) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > base > > other attached packages: > ?[1] ChromHeatMap_1.2.0 ? ? ? ? ? ? ? ? hgu95av2.db_2.4.1 > ?[3] org.Hs.eg.db_2.4.1 ? ? ? ? ? ? ? ? ALL_1.4.7 > ?[5] org.Mm.eg.db_2.4.1 ? ? ? ? ? ? ? ? RSQLite_0.8-4 > ?[7] DBI_0.2-5 ? ? ? ? ? ? ? ? ? ? ? ? ?BSgenome.Mmusculus.UCSC.mm9_1.3.16 > ?[9] BSgenome_1.16.5 ? ? ? ? ? ? ? ? ? ?Biostrings_2.16.7 > [11] GenomicRanges_1.0.5 ? ? ? ? ? ? ? ?IRanges_1.6.8 > [13] vsn_3.16.0 ? ? ? ? ? ? ? ? ? ? ? ? limma_3.4.4 > [15] gplots_2.7.4 ? ? ? ? ? ? ? ? ? ? ? caTools_1.10 > [17] bitops_1.0-4.1 ? ? ? ? ? ? ? ? ? ? gdata_2.7.1 > [19] gtools_2.6.1 ? ? ? ? ? ? ? ? ? ? ? DESeq_1.0.4 > [21] locfit_1.5-6 ? ? ? ? ? ? ? ? ? ? ? akima_0.5-4 > [23] geneplotter_1.26.0 ? ? ? ? ? ? ? ? lattice_0.18-5 > [25] annotate_1.26.1 ? ? ? ? ? ? ? ? ? ?AnnotationDbi_1.10.0 > [27] Biobase_2.8.0 > > loaded via a namespace (and not attached): > ?[1] affy_1.26.1 ? ? ? ? ? affyio_1.16.0 ? ? ? ? genefilter_1.30.0 > preprocessCore_1.10.0 > ?[5] RColorBrewer_1.0-2 ? ?RCurl_1.3-1 ? ? ? ? ? rtracklayer_1.8.1 > splines_2.11.0 > ?[9] survival_2.35-8 ? ? ? tools_2.11.0 ? ? ? ? ?XML_2.8-1 > xtable_1.5-6 > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > mmuratet at hudsonalpha.org > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > > > > >

Hi there I am completely lost on how to map from probe to gene using nimblegen data. Where can I find a tutorial or some kind of help. I see that I need to generate a package, but I need my tabular file in a specific order, does anyone knows what this order may be? Cheers Marcelo Em 20 de agosto de 2010 00:50, Mark Cowley <m.cowley at="" garvan.org.au=""> escreveu: > Hi Marcelo, > take a look at the annotation packages here: http://bioconductor.org/packages/release/AnnotationData.html > > you'll need to do the mapping from probe to gene before running heatmap.2, since heatmap.2 won't do that conversion for you > > cheers, > Mark > > On 20/08/2010, at 12:09 AM, Marcelo Brand?o wrote: > >> Thanks Mark. >> >> Now, the data makes sense. >> I draw the results on a heatmap (heatmap.2 from gplots), do you have >> any idea on how to change the probes names to geneID? I am using >> Nimblegen data and have an NDF file with all annotation. >> >> Cheers and thanks again >> >> Marcelo >> >> Em 19 de agosto de 2010 01:29, Mark Cowley <m.cowley at="" garvan.org.au=""> escreveu: >>> hi Marcelo, >>> >>> If you use that design matrix, then you'll need to also fit contrasts >>>> designEsp <- cbind(controle=c(1,1,1,0,0,0),experimento=c(0,0,0,1,1,1)) >>>> fitEsp <- lmFit(exprs(summarized),designEsp) >>> contr.matrix <- c(-1,1) >>> fitEsp <- contrasts.fit(fitEsp, contr.matrix) >>>> fitEsp <- eBayes(fitEsp) >>>> topTable(fitEsp,coef=1, adjust = "fdr", n = 10) >>> >>> or use this design >>>> designEsp2 <- cbind(intercept=c(1,1,1,1,1,1),expvscon=c(0,0,0,1,1,1)) >>>> fitEsp2 <- lmFit(exprs(summarized),designEsp2) >>>> fitEsp2 <- eBayes(fitEsp2) >>>> topTable(fitEsp2,coef=2, adjust = "fdr", n = 10) >>> >>> cheers, >>> Mark >>> On 19/08/2010, at 10:59 AM, Marcelo Brand?o wrote: >>> >>>> Hello all! >>>> I am analyzing a set with 6 microarrays, 3 controls and 3 >>>> experimentals. I am interested in look after differentially expressed >>>> genes. My doubt, among a lot of else, is if my experiment is designed >>>> correctly. I am currently using the following comands: >>>> >>>> designEsp <- cbind(controle=c(1,1,1,0,0,0),experimento=c(0,0,0,1,1,1)) >>>> fitEsp <- lmFit(exprs(summarized),designEsp) >>>> fitEsp <- eBayes(fitEsp) >>>> topTable(fitEsp,coef=2, adjust = "fdr", n = 10) >>>> >>>> is it the best way to infer different expression? I am using nimblegen >>>> microarrays. >>>> >>>> Thanks in advance. >>>> >>>> Marcelo >>>> >>>> -- >>>> Marcelo Mendes Brand?o >>>> Postdoc fellow >>>> Laborat?rio de Biologia Molecular de Plantas - ESALQ/USP >>>> Website: http://bioinfo.esalq.usp.br >>>> AtPIN: http://bioinfo.esalq.usp.br/atpin >>>> SKYPE: mmbrand >>>> Tel: (+55) 19 3429 4442 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> >> >> -- >> Marcelo Mendes Brand?o >> Postdoc fellow >> Laborat?rio de Biologia Molecular de Plantas - ESALQ/USP >> Website: http://bioinfo.esalq.usp.br >> AtPIN: http://bioinfo.esalq.usp.br/atpin >> SKYPE: mmbrand >> Tel: (+55) 19 3429 4442 > > -- Marcelo Mendes Brand?o Postdoc fellow Laborat?rio de Biologia Molecular de Plantas - ESALQ/USP Website: http://bioinfo.esalq.usp.br AtPIN: http://bioinfo.esalq.usp.br/atpin SKYPE: mmbrand Tel: (+55) 19 3429 4442