Holly,

Could you please try to run the example code in the help page (?makeVennDiagram) ? If the example works as expected, then please send me the .Rdata with the two peak files.

For setting the totalTest, please refer to faq at http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/ChIPpeakAnno-BioC2011.pdf

The p.value is obtained from hypergeometric test.

Best regards,

Julie


On 8/1/12 11:25 AM, "Holly" <xyang2@uchicago.edu> wrote:


Julie,

 I think the release may not be the issue. The Bioconductor 2.10 is designed for R2.15.
 I installed the package within R as following:

>   source("http://bioconductor.org/biocLite.R" <http://bioconductor.org/biocLite.R> )
BiocInstaller version 1.4.7, ?biocLite for help
>     biocLite("ChIPpeakAnno")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.7.
Installing package(s) 'ChIPpeakAnno'
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/2.15/ChIPpeakAnno_2.4.0.zip'
Content type 'application/zip' length 8028874 bytes (7.7 Mb)
opened URL
downloaded 7.7 Mb

package ‘ChIPpeakAnno’ successfully unpacked and MD5 sums checked

BTW, should we consider the "totalTest" as a background number of peaks in the whole genome that a transcription factor could bind?
Do you use FET to calculate the p-value?

Thanks,
Holly

 On 8/1/2012 7:52 AM, Zhu, Lihua (Julie) wrote:


 Re: more question about makeVennDiagram Holly,

 According to your session information, you are using R dev and released version of ChIPpeakAnno. Please either updpate ChIPpeakAnno to dev version or use R released version instead. Please let us know if the issue goes away. Thanks!

 Best regards,

 Julie



 On 8/1/12 12:38 AM, "Holly" <xyang2@uchicago.edu> wrote:


Hey, Julie,

  After reading the message at https://stat.ethz.ch/pipermail/bioconductor/2010-June/033941.html
  I enlarged the "totalTest", but still got strange results as following. Could you please help to debug?

  My Peaks_A has 55872 reads, while Peaks_B has 1316 reads.
  Thanks,
  Holly


  > makeVennDiagram(RangedDataList(Peaks_A, Peaks_B), NameOfPeaks=c("A", "B"),
  +        maxgap=0, totalTest=50000000, cex = 1, counts.col = "red",useFeature=FALSE)
  $p.value
  [1] 0

  $vennCounts
          A     B   Counts
  [1,]    0    0 50000062
  [2,]    0    1      -62
  [3,]    1    0      -62
  [4,]    1    1       62
  attr(,"class")
  [1] "VennCounts"

  Warning messages:
  1: In findOverlappingPeaks(Peaks[[1]], Peaks[[2]], NameOfPeaks1 = NameOfPeaks[1],  :
    Please use select instead of multiple!
  2: In findVennCounts(Peaks = Peaks, NameOfPeaks = NameOfPeaks, maxgap = maxgap,  :
    negative counts generated when multiple peaks overlap with one peak!


 > sessionInfo()
 R version 2.15.0 (2012-03-30)
  Platform: x86_64-pc-mingw32/x64 (64-bit)

  locale:
  [1] LC_COLLATE=English_United States.1252
  [2] LC_CTYPE=English_United States.1252
  [3] LC_MONETARY=English_United States.1252
  [4] LC_NUMERIC=C
  [5] LC_TIME=English_United States.1252

  attached base packages:
  [1] grid      stats     graphics  grDevices utils     datasets  methods
  [8] base

  other attached packages:
   [1] ChIPpeakAnno_2.4.0                  limma_3.12.1
   [3] org.Hs.eg.db_2.7.1                  GO.db_2.7.1
   [5] RSQLite_0.11.1                      DBI_0.2-5
   [7] AnnotationDbi_1.18.1                BSgenome.Ecoli.NCBI.20080805_1.3.17
   [9] BSgenome_1.24.0                     GenomicRanges_1.8.9
  [11] Biostrings_2.24.1                   IRanges_1.14.4
  [13] multtest_2.12.0                     Biobase_2.16.0
  [15] biomaRt_2.12.0                      BiocGenerics_0.2.0
  [17] gplots_2.11.0                       MASS_7.3-17
  [19] KernSmooth_2.23-7                   caTools_1.13
  [21] bitops_1.0-4.1                      gdata_2.11.0
  [23] gtools_2.7.0                        BiocInstaller_1.4.7

  loaded via a namespace (and not attached):
  [1] RCurl_1.91-1.1   splines_2.15.0   stats4_2.15.0    survival_2.36-12
  [5] tools_2.15.0     XML_3.9-4.1








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