for this intensive task you will want to look at the devel version of GGtools where the multffCT function is provided to use multicore and ff to help manage full cis-trans eQTL searches. this has very few users so far so please comment if you find problems. On Tue, Jan 19, 2010 at 8:11 AM, Paul Geeleher <paulgeeleher at="" gmail.com=""> wrote: > Thanks Vincent, > > That worked great. I set entrez gene ids as my featureNames() and > "org.Hs.eg.db" as my annotation platform. > > featureNames(ceuExprSet) <- as.character(entrezIds) > annotation(ceuExprSet) <- "org.Hs.eg.db" > > I seems to be working now. > > One question, if I run the analysis for all genes across all SNPs (I > calculate it will take about 2 weeks) does the gwSnpTests() function correct > for multiple testing? I'm specifically looking for genes related to miRNA > processing so maybe I'd be best to subset on those? Although I'd still be > interested to see what cropped with the full geneset... > > Paul > > On Mon, Jan 18, 2010 at 2:37 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> > wrote: >> >> Thanks for additional info; let's keep this on the list. ?It turns out >> that this use case is not covered by current code. ?The most common >> expression featureNames in applications are array probe(set) >> identifiers. ?gwSnpTests handles the situation where the GeneSet for >> the response has "biologically oriented" identifiers like HUGO symbols >> (so a relevant GeneSet would have geneIdType SymbolIdentifier()), but >> the expression data rows are labeled with annotation-oriented >> identifiers (with geneIdType AnnotationIdentifier([platform >> specification]). >> >> Because we don't have formal types for featureNames output (we just >> get character strings) it is hard for me to check for this situation. >> I will think about a way out that handles your use case; for now, if >> you could map your expression featureNames to those of some relevant >> annotated platform, you could go forward with the same call upon >> setting the annotation slot of the smlSet appropriately. ?In >> particular if you wanted to use Entrez IDs, it should work to use >> org.[something].eg.db for the annotation (assuming you did not use >> some bioc-annotated microarray platform to get your expression data) >> but I have not tried this. >> >> On Mon, Jan 18, 2010 at 7:32 AM, Paul Geeleher <paulgeeleher at="" gmail.com=""> >> wrote: >> > Hi Vincent, >> > >> > Thanks for your reply. It doesn't look to me like that's the problem >> > though. >> > I've pasted some code/output below. Is there anything else that springs >> > to >> > mind? It'd be great if I could get this working: >> > >> >> exprs(hapSmlSet)[1:5, 1:5] >> > ???????? NA06985? NA07048? NA07055? NA07056? NA07345 >> > TTLL10? 5.804398 6.111066 6.015460 6.077223 6.052570 >> > B3GALT6 6.900609 6.614555 6.770701 6.688613 6.570467 >> > SCNN1D? 5.698484 6.148147 5.777978 5.892331 6.073576 >> > PUSL1?? 7.010970 6.970204 7.045875 7.424906 6.785346 >> > VWA1??? 6.559377 6.689263 6.447208 6.574919 5.988598 >> > >> >> gs1 = GeneSet(c("TTLL10", "VWA1")) >> >> geneIdType(gs1) = SymbolIdentifier() >> >> >> >> >> >> outData <- gwSnpTests(gs1~male, hapSmlSet) >> > Error in data.frame(get(pname), pData(sms)) : >> > ? arguments imply differing number of rows: 0, 87 >> >> >> > >> > >> > Thanks, >> > >> > Paul. >> > >> > >> > >> > On Fri, Jan 15, 2010 at 3:36 PM, Vincent Carey >> > <stvjc at="" channing.harvard.edu=""> >> > wrote: >> >> >> >> The best possible explanation is that gs1 includes a probe set id that >> >> is not present in exprs(hapSmlSet) >> >> get(pname) is attempting to retrieve the expression values for probes >> >> enumerated in gs1 >> >> >> >> i am sorry that the error message is cryptic; this package is >> >> undergoing renovation to improve performance >> >> and user interface. ?continue to post your concerns to the list; don't >> >> forget sessionInfo() >> >> >> >> On Fri, Jan 15, 2010 at 8:37 AM, Paul Geeleher <paulgeeleher at="" gmail.com=""> >> >> wrote: >> >> > Hi List, >> >> > >> >> > I'm trying to run an association analysis with GGTools. I'm getting >> >> > an >> >> > error >> >> > when I run: >> >> > >> >> >> outData <- gwSnpTests(gs1~male, hapSmlSet) >> >> > Error in data.frame(get(pname), pData(sms)) : >> >> > arguments imply differing number of rows: 0, 87 >> >> > >> >> > There are 87 samples in my analysis so that explains that, but I >> >> > don't >> >> > know >> >> > what "get(pname)" is doing or why it is returning 0. I'm guessing >> >> > I've >> >> > something missing somewhere in the data I've loaded. >> >> > >> >> > I can provide more information if necessary. >> >> > >> >> > Thanks, >> >> > >> >> > Paul >> >> > >> >> > >> >> > >> >> > R version 2.10.1 (2009-12-14) >> >> > x86_64-pc-linux-gnu >> >> > >> >> > locale: >> >> > ?[1] LC_CTYPE=en_IE.UTF-8 ? ? ? LC_NUMERIC=C >> >> > ?[3] LC_TIME=en_IE.UTF-8 ? ? ? ?LC_COLLATE=en_IE.UTF-8 >> >> > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_IE.UTF-8 >> >> > ?[7] LC_PAPER=en_IE.UTF-8 ? ? ? LC_NAME=C >> >> > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> >> > [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C >> >> > >> >> > attached base packages: >> >> > [1] splines ? stats ? ? graphics ?grDevices utils ? ? datasets >> >> > ?methods >> >> > [8] base >> >> > >> >> > other attached packages: >> >> > ?[1] org.Hs.eg.db_2.3.6 ?GGtools_3.4.0 ? ? ? rpart_3.1-46 >> >> > ?[4] Biostrings_2.14.0 ? IRanges_1.4.0 ? ? ? RColorBrewer_1.0-2 >> >> > ?[7] GGBase_3.6.0 ? ? ? ?RSQLite_0.8-0 ? ? ? DBI_0.2-5 >> >> > [10] snpMatrix_1.10.3 ? ?survival_2.35-8 ? ? GSEABase_1.8.0 >> >> > [13] graph_1.24.1 ? ? ? ?annotate_1.24.0 ? ? AnnotationDbi_1.8.0 >> >> > [16] GEOquery_2.10.0 ? ? RCurl_1.3-0 ? ? ? ? bitops_1.0-4.1 >> >> > [19] Biobase_2.6.0 >> >> > >> >> > loaded via a namespace (and not attached): >> >> > [1] annaffy_1.18.0 tcltk_2.10.1 ? tools_2.10.1 ? XML_2.6-0 >> >> > xtable_1.5-6 >> >> >> >> >> > >> >> > >> >> > -- >> >> > Paul Geeleher >> >> > School of Mathematics, Statistics and Applied Mathematics >> >> > National University of Ireland >> >> > Galway >> >> > Ireland >> >> > >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> > >> >> > _______________________________________________ >> >> > 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 >> >> > >> > >> > >> > >> > -- >> > Paul Geeleher >> > School of Mathematics, Statistics and Applied Mathematics >> > National University of Ireland >> > Galway >> > Ireland >> > >> > > > > > -- > Paul Geeleher > School of Mathematics, Statistics and Applied Mathematics > National University of Ireland > Galway > Ireland > >

On Tue, Jan 19, 2010 at 8:11 AM, Paul Geeleher <paulgeeleher at="" gmail.com=""> wrote: > Thanks Vincent, > > That worked great. I set entrez gene ids as my featureNames() and > "org.Hs.eg.db" as my annotation platform. > > featureNames(ceuExprSet) <- as.character(entrezIds) > annotation(ceuExprSet) <- "org.Hs.eg.db" > > I seems to be working now. > > One question, if I run the analysis for all genes across all SNPs (I > calculate it will take about 2 weeks) does the gwSnpTests() function correct > for multiple testing? I'm specifically looking for genes related to miRNA no, there is no multiple testing adjustment in these procedures > processing so maybe I'd be best to subset on those? Although I'd still be > interested to see what cropped with the full geneset... > > Paul > > On Mon, Jan 18, 2010 at 2:37 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> > wrote: >> >> Thanks for additional info; let's keep this on the list. ?It turns out >> that this use case is not covered by current code. ?The most common >> expression featureNames in applications are array probe(set) >> identifiers. ?gwSnpTests handles the situation where the GeneSet for >> the response has "biologically oriented" identifiers like HUGO symbols >> (so a relevant GeneSet would have geneIdType SymbolIdentifier()), but >> the expression data rows are labeled with annotation-oriented >> identifiers (with geneIdType AnnotationIdentifier([platform >> specification]). >> >> Because we don't have formal types for featureNames output (we just >> get character strings) it is hard for me to check for this situation. >> I will think about a way out that handles your use case; for now, if >> you could map your expression featureNames to those of some relevant >> annotated platform, you could go forward with the same call upon >> setting the annotation slot of the smlSet appropriately. ?In >> particular if you wanted to use Entrez IDs, it should work to use >> org.[something].eg.db for the annotation (assuming you did not use >> some bioc-annotated microarray platform to get your expression data) >> but I have not tried this. >> >> On Mon, Jan 18, 2010 at 7:32 AM, Paul Geeleher <paulgeeleher at="" gmail.com=""> >> wrote: >> > Hi Vincent, >> > >> > Thanks for your reply. It doesn't look to me like that's the problem >> > though. >> > I've pasted some code/output below. Is there anything else that springs >> > to >> > mind? It'd be great if I could get this working: >> > >> >> exprs(hapSmlSet)[1:5, 1:5] >> > ???????? NA06985? NA07048? NA07055? NA07056? NA07345 >> > TTLL10? 5.804398 6.111066 6.015460 6.077223 6.052570 >> > B3GALT6 6.900609 6.614555 6.770701 6.688613 6.570467 >> > SCNN1D? 5.698484 6.148147 5.777978 5.892331 6.073576 >> > PUSL1?? 7.010970 6.970204 7.045875 7.424906 6.785346 >> > VWA1??? 6.559377 6.689263 6.447208 6.574919 5.988598 >> > >> >> gs1 = GeneSet(c("TTLL10", "VWA1")) >> >> geneIdType(gs1) = SymbolIdentifier() >> >> >> >> >> >> outData <- gwSnpTests(gs1~male, hapSmlSet) >> > Error in data.frame(get(pname), pData(sms)) : >> > ? arguments imply differing number of rows: 0, 87 >> >> >> > >> > >> > Thanks, >> > >> > Paul. >> > >> > >> > >> > On Fri, Jan 15, 2010 at 3:36 PM, Vincent Carey >> > <stvjc at="" channing.harvard.edu=""> >> > wrote: >> >> >> >> The best possible explanation is that gs1 includes a probe set id that >> >> is not present in exprs(hapSmlSet) >> >> get(pname) is attempting to retrieve the expression values for probes >> >> enumerated in gs1 >> >> >> >> i am sorry that the error message is cryptic; this package is >> >> undergoing renovation to improve performance >> >> and user interface. ?continue to post your concerns to the list; don't >> >> forget sessionInfo() >> >> >> >> On Fri, Jan 15, 2010 at 8:37 AM, Paul Geeleher <paulgeeleher at="" gmail.com=""> >> >> wrote: >> >> > Hi List, >> >> > >> >> > I'm trying to run an association analysis with GGTools. I'm getting >> >> > an >> >> > error >> >> > when I run: >> >> > >> >> >> outData <- gwSnpTests(gs1~male, hapSmlSet) >> >> > Error in data.frame(get(pname), pData(sms)) : >> >> > arguments imply differing number of rows: 0, 87 >> >> > >> >> > There are 87 samples in my analysis so that explains that, but I >> >> > don't >> >> > know >> >> > what "get(pname)" is doing or why it is returning 0. I'm guessing >> >> > I've >> >> > something missing somewhere in the data I've loaded. >> >> > >> >> > I can provide more information if necessary. >> >> > >> >> > Thanks, >> >> > >> >> > Paul >> >> > >> >> > >> >> > >> >> > R version 2.10.1 (2009-12-14) >> >> > x86_64-pc-linux-gnu >> >> > >> >> > locale: >> >> > ?[1] LC_CTYPE=en_IE.UTF-8 ? ? ? LC_NUMERIC=C >> >> > ?[3] LC_TIME=en_IE.UTF-8 ? ? ? ?LC_COLLATE=en_IE.UTF-8 >> >> > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_IE.UTF-8 >> >> > ?[7] LC_PAPER=en_IE.UTF-8 ? ? ? LC_NAME=C >> >> > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> >> > [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C >> >> > >> >> > attached base packages: >> >> > [1] splines ? stats ? ? graphics ?grDevices utils ? ? datasets >> >> > ?methods >> >> > [8] base >> >> > >> >> > other attached packages: >> >> > ?[1] org.Hs.eg.db_2.3.6 ?GGtools_3.4.0 ? ? ? rpart_3.1-46 >> >> > ?[4] Biostrings_2.14.0 ? IRanges_1.4.0 ? ? ? RColorBrewer_1.0-2 >> >> > ?[7] GGBase_3.6.0 ? ? ? ?RSQLite_0.8-0 ? ? ? DBI_0.2-5 >> >> > [10] snpMatrix_1.10.3 ? ?survival_2.35-8 ? ? GSEABase_1.8.0 >> >> > [13] graph_1.24.1 ? ? ? ?annotate_1.24.0 ? ? AnnotationDbi_1.8.0 >> >> > [16] GEOquery_2.10.0 ? ? RCurl_1.3-0 ? ? ? ? bitops_1.0-4.1 >> >> > [19] Biobase_2.6.0 >> >> > >> >> > loaded via a namespace (and not attached): >> >> > [1] annaffy_1.18.0 tcltk_2.10.1 ? tools_2.10.1 ? XML_2.6-0 >> >> > xtable_1.5-6 >> >> >> >> >> > >> >> > >> >> > -- >> >> > Paul Geeleher >> >> > School of Mathematics, Statistics and Applied Mathematics >> >> > National University of Ireland >> >> > Galway >> >> > Ireland >> >> > >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> > >> >> > _______________________________________________ >> >> > 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 >> >> > >> > >> > >> > >> > -- >> > Paul Geeleher >> > School of Mathematics, Statistics and Applied Mathematics >> > National University of Ireland >> > Galway >> > Ireland >> > >> > > > > > -- > Paul Geeleher > School of Mathematics, Statistics and Applied Mathematics > National University of Ireland > Galway > Ireland > >