Hi Khademul, Regarding the speed concern with very big bed files, splitting the files chromosome by chromosome would help if you can run R in a cluster. Regarding p-value for overlap, set totalTest appropriately is critical. Please refer to the posts. http://permalink.gmane.org/gmane.science.biology.informatics.conductor /29476 http://permalink.gmane.org/gmane.science.biology.informatics.conductor /30115 Kind regards, Julie On 8/9/10 6:02 AM, "Khademul Islam" <khademul.islam@gmail.com> wrote: Hi Julie, Nice to see published ChIPpeakAnno paper. I was trying to do overlapping between my ChIPseq peak bed file (peak1: ~3100 peaks) and Exon_Intron Boundary bed file ( peak2: ~400000 ). There are two concerns: 1. Its takes too long time (overnight) to calculate all these even with powerful machine........., specially when one bed file is too big. 2. It produced "NaN" for p-value $p.value [1] NaN $vennCounts peak1 peak2 Counts [1,] 0 0 -398821 [2,] 0 1 395828 [3,] 1 0 2253 [4,] 1 1 840 attr(,"class") [1] "VennCounts" So it counts "-" (minus) -398821 ??? There were 22 warnings but no other error. Warning says that it produces "NaN" I pasted warnings below. I wanted to attach the bed files if you need to check, but its too large. Well, in case if you need it, let me know, I will upload it in FTP site. I got the venn diagram pic without any problem (attached). Command line was: ol <- findOverlappingPeaks(peaks1, peaks2, maxgap=1, multiple=F, NameOfPeaks1="Peak1", NameOfPeaks2="Peak2") vdg <- makeVennDiagram(RangedDataList(peaks1, peaks2), NameOfPeaks=c("peak1", "peak2"), maxgap=0, totalTest=100, cex = 1, counts.col = "red") > dev.copy2eps() > vdg So, my question is, how can I get proper p-value from the overlap, what I have to do to fix it? Thank you, Khademul > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.4.1 ..... > 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'. 4: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 5: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 6: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 7: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 8: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 9: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 10: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 11: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 12: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 13: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 14: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 15: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 16: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 17: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 18: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 19: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 20: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 21: In .local(query, subject, maxgap, minoverlap, type, select, ... : argument 'multiple' is deprecated; use 'select'. 22: In phyper(q, m, n, k, lower.tail, log.p) : NaNs produced [[alternative HTML version deleted]]