Hello All, I ran the following function and received the following output but it is unclear to me why I have a negative number for vennCounts (and no p-value). Any ideas? My output for the example in the vignette is correct but running the function with my data I am getting the following: > makeVennDiagram(RangedDataList(smallAnnoTFA, smallAnnoTFB), NameOfPeaks=c("TFA", "TFB"), maxgap = 0, totalTest= 100, cex = 1, counts.col = "purple") $p.value [1] NaN $vennCounts TFA TFB Counts [1,] 0 0 -2667 [2,] 0 1 755 [3,] 1 0 1334 [4,] 1 1 678 attr(,"class") [1] "VennCounts" There were 17 warnings (use warnings() to see them) > warnings() Warning messages: 1: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 2: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 3: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. Thank you for any help. Noah > sessionInfo() R version 2.11.0 (2010-04-22) i386-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] org.Sc.sgd.db_2.4.1 rtracklayer_1.8.1 [3] RCurl_1.3-1 bitops_1.0-4.1 [5] Starr_1.4.0 affxparser_1.20.0 [7] affy_1.26.0 Ringo_1.12.0 [9] Matrix_0.999375-38 lattice_0.18-5 [11] RColorBrewer_1.0-2 ChIPpeakAnno_1.4.0 [13] limma_3.4.0 org.Hs.eg.db_2.4.1 [15] GO.db_2.4.1 RSQLite_0.8-4 [17] DBI_0.2-5 AnnotationDbi_1.10.0 [19] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.0 [21] GenomicRanges_1.0.1 Biostrings_2.16.0 [23] IRanges_1.6.0 multtest_2.4.0 [25] Biobase_2.8.0 biomaRt_2.4.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.0 genefilter_1.30.0 MASS_7.3-5 [5] preprocessCore_1.10.0 pspline_1.0-14 splines_2.11.0 survival_2.35-8 [9] tools_2.11.0 XML_2.8-1 xtable_1.5-6 >

Hi Noah, Totaltest specifies the total number of tests performed to obtain the list of peaks. It should be larger than the largest number of peaks in A and B. 100 is too small. Thanks! Best regards, Julie On 6/12/10 9:04 PM, "Noah Dowell" <noahd at="" ucla.edu=""> wrote: > Hello All, > > I ran the following function and received the following output but it is > unclear to me why I have a negative number for vennCounts (and no p-value). > Any ideas? My output for the example in the vignette is correct but running > the function with my data I am getting the following: > >> makeVennDiagram(RangedDataList(smallAnnoTFA, smallAnnoTFB), >> NameOfPeaks=c("TFA", "TFB"), maxgap = 0, totalTest= 100, cex = 1, counts.col >> = "purple") > $p.value > [1] NaN > > $vennCounts > TFA TFB Counts > [1,] 0 0 -2667 > [2,] 0 1 755 > [3,] 1 0 1334 > [4,] 1 1 678 > attr(,"class") > [1] "VennCounts" > > There were 17 warnings (use warnings() to see them) > >> warnings() > Warning messages: > 1: In .local(query, subject, maxgap, minoverlap, type, select, ... : > argument 'multiple' is deprecated; use 'select'. > 2: In .local(query, subject, maxgap, minoverlap, type, select, ... : > argument 'multiple' is deprecated; use 'select'. > 3: In .local(query, subject, maxgap, minoverlap, type, select, ... : > argument 'multiple' is deprecated; use 'select'. > > > > Thank you for any help. > > Noah > > > > > > > >> sessionInfo() > R version 2.11.0 (2010-04-22) > i386-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] org.Sc.sgd.db_2.4.1 rtracklayer_1.8.1 > [3] RCurl_1.3-1 bitops_1.0-4.1 > [5] Starr_1.4.0 affxparser_1.20.0 > [7] affy_1.26.0 Ringo_1.12.0 > [9] Matrix_0.999375-38 lattice_0.18-5 > [11] RColorBrewer_1.0-2 ChIPpeakAnno_1.4.0 > [13] limma_3.4.0 org.Hs.eg.db_2.4.1 > [15] GO.db_2.4.1 RSQLite_0.8-4 > [17] DBI_0.2-5 AnnotationDbi_1.10.0 > [19] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.0 > [21] GenomicRanges_1.0.1 Biostrings_2.16.0 > [23] IRanges_1.6.0 multtest_2.4.0 > [25] Biobase_2.8.0 biomaRt_2.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.0 genefilter_1.30.0 > MASS_7.3-5 > [5] preprocessCore_1.10.0 pspline_1.0-14 splines_2.11.0 > survival_2.35-8 > [9] tools_2.11.0 XML_2.8-1 xtable_1.5-6 >> > _______________________________________________ > 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 >