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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