Dear all, i have a question on the "vennCounts" function. Using this function on "results" value: > vennCounts(results) [hda+str]-[ref] [ref+str]-[ref] [hda+str]-[ref+str] Counts [1,] 0 0 0 21496 [2,] 0 0 1 0 [3,] 0 1 0 12 [4,] 0 1 1 0 [5,] 1 0 0 32 [6,] 1 0 1 1 [7,] 1 1 0 34 [8,] 1 1 1 0 attr(,"class") [1] "VennCounts" what i shoul need is a way to understand which genes are in the [7,] line from the "[hda+str]-[ref] vs [ref+str]-[ref]". The only think i know is the number that should be 34, but i would like to obtain a list of the 34 genes. best regards. > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-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] AnnotationDbi_1.14.1 Biobase_2.12.1 GenomicFeatures_1.4.2 [4] GenomicRanges_1.4.1 IRanges_1.10.0 limma_3.8.1 [7] biomaRt_2.8.0 loaded via a namespace (and not attached): [1] Biostrings_2.20.0 BSgenome_1.20.0 DBI_0.2-5 RCurl_1.5-0 [5] RSQLite_0.9-4 rtracklayer_1.12.3 tools_2.13.0 XML_3.2-0 -- ----------------------------------------------------- Dr. Alberto Goldoni Parma, Italy

Hi Alberto, On 6/21/2011 12:53 PM, Alberto Goldoni wrote: > Dear all, > i have a question on the "vennCounts" function. > > Using this function on "results" value: > >> vennCounts(results) > [hda+str]-[ref] [ref+str]-[ref] [hda+str]-[ref+str] Counts > [1,] 0 0 0 21496 > [2,] 0 0 1 0 > [3,] 0 1 0 12 > [4,] 0 1 1 0 > [5,] 1 0 0 32 > [6,] 1 0 1 1 > [7,] 1 1 0 34 > [8,] 1 1 1 0 > attr(,"class") > [1] "VennCounts" > > what i shoul need is a way to understand which genes are in the [7,] > line from the "[hda+str]-[ref] vs [ref+str]-[ref]". > > The only think i know is the number that should be 34, but i would > like to obtain a list of the 34 genes. You will need to use the results object to do that. The results object will be a matrix with three columns and as many rows as genes in your comparison. So e.g., the first column will represent the [hda+str]-[ref] comparison, and will consist of 1's, 0's and -1's. If you do something like sum(abs(results[,1]) == 1 & abs(results([,2]) == 1) you should get 34. Given that information, I leave it to you to figure out how to subset your genes. Best, Jim > > best regards. > >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-linux-gnu (64-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] AnnotationDbi_1.14.1 Biobase_2.12.1 GenomicFeatures_1.4.2 > [4] GenomicRanges_1.4.1 IRanges_1.10.0 limma_3.8.1 > [7] biomaRt_2.8.0 > > loaded via a namespace (and not attached): > [1] Biostrings_2.20.0 BSgenome_1.20.0 DBI_0.2-5 RCurl_1.5-0 > [5] RSQLite_0.9-4 rtracklayer_1.12.3 tools_2.13.0 XML_3.2-0 > -- 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