[BioC] Question on makeVennDiagram function in ChIPpeakAnno

[Noah Dowell]

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         
>