Hi Mali, Thanks for the bug report. Fixed now in svn, which will be propagated to the devel version in 24 hours or so. Best, Jim On 3/17/2011 5:11 AM, mali salmon wrote: > Thanks a lot Jim, it was really helpful!!! > I debugged the function and found the problem. > My lmFit object, and hence the "tables" object contain gene symbols which I > added to the lmFit object in some point. In the code when it reaches the > line "aafTable(`Fold Change` = round(fld, 2))" it actually reads the symbols > instead of the fold change. > May I suggest to replace the line "fld<-tables[[i]][,2]" with > "fld<-tables[[i]][,"logFC"], this can prevent the error in the future. > > I solved this problem and encountered another one, and after debugging I > think I found a small bug in the code. > The problem appears when I set in the command line "tstat = FALSE". The > first hrml file for the first contrast is generated successfully, but when > it comes to generate the "testtable" for the second contrast I get the error > > > "Error in merge.aafTable(testtable, aafTable(`p-value` = > round(tables[[i]][, : > The tables must have the same number of rows" > > This is because when tstat=FALSE, the testtable is not reset and updated to > the new comparison. > > >if (tstat) testtable<- aafTable(`t-statistic` = round(tables[[i]][, "t"], > 2)) > >if (pval) { > > if (!exists("testtable")) { > > testtable<- aafTable(`p-value` = round(tables[[i]][, > > "adj.P.Val"], 3)) > > } > > else { > > testtable<- merge(testtable, aafTable(`p-value` = > round(tables[[i]][, > > "adj.P.Val"], 3))) > > } >> } > > When I set "tstat=TRUE" everything is OK > > All the best > Mali > > > > > > > > This > All the best > Mali > > On Wed, Mar 16, 2011 at 3:32 PM, James W. MacDonald > <jmacdon at="" med.umich.edu="">wrote: > >> Hi Mali, >> >> >> On 3/16/2011 3:23 AM, mali salmon wrote: >> >>> Hi All >>> I am analysing affymetrix data, and I am trying to use "limma2annaffy" >>> function from "affycoretools" package to create html tables. >>> When I run the following command: >>> >>> limma2annaffy(eset, fit2, design, cont.matrix,lib="hgu133a2" , adjust = >>>> >>> "fdr", >>> anncols = aaf.handler()[c(1:3, 4:5, 11:12)], pfilt = >>> 0.05,fldfilt=2,tstat = FALSE, pval = TRUE, FC = TRUE, >>> expression = TRUE, html = TRUE, text = FALSE, save = FALSE) >>> I get the error: >>> "Error in round(fld, 2) : Non-numeric argument to mathematical function" >>> >>> In order to understand why I get this error, I have tried to generate the >>> "tables" object from the limma2annaffy code. >>> However, when I get to "tableFilt" function, R can't find it although the >>> package is loaded. >>> >> >> The easiest way to debug a function is to do >> >> debug(limma2annaffy) >> >> then run the function call. You can then step through the execution of the >> function line by line, and look at the intermediate objects being made, such >> as the tables list. Since you will be debugging from within the package >> namespace, all functions will be available to you. >> >> Note however that the tableFilt() function simply takes the output from >> topTable() and then filters based on the p-value and fold change you >> supplied. The error indicates that you are getting non-numeric values in the >> second column of your topTable() output, which is unexpected. >> >> >> >>> When I type ?tableFilt I get the documentation, but when I try to view the >>> code I get >>> >>>> tableFilt >>>> >>> Error: object 'tableFilt' not found >>> >> >> That's because this package has a namespace, and the tableFilt() function >> isn't exported. You can access unexported functions using :::, e.g., >> affycoretools:::tableFilt. >> >> Best, >> >> Jim >> >> >> >>> Any ideas? >>> Thanks >>> Mali >>> >>> >>> sessionInfo() >>>> >>> R version 2.12.1 (2010-12-16) >>> Platform: i386-redhat-linux-gnu (32-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 >>> [4] annotate_1.28.0 affycoretools_1.22.0 KEGG.db_2.4.5 >>> [7] GO.db_2.4.5 RSQLite_0.9-4 DBI_0.2-5 >>> [10] AnnotationDbi_1.12.0 simpleaffy_2.26.1 gcrma_2.22.0 >>> [13] genefilter_1.32.0 hgu133a2cdf_2.7.0 affy_1.28.0 >>> [16] Biobase_2.10.0 limma_3.6.9 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 >>> [4] Category_2.16.1 GOstats_2.16.0 graph_1.28.0 >>> [7] GSEABase_1.12.2 IRanges_1.8.9 preprocessCore_1.12.0 >>> [10] RBGL_1.26.0 RCurl_1.5-0 splines_2.12.1 >>> [13] survival_2.36-2 tcltk_2.12.1 tools_2.12.1 >>> [16] XML_3.2-0 xtable_1.5-6 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues