[BioC] Question on makeVennDiagram function in ChIPpeakAnno

[Zhu, Julie]

Hi Noah,

Totaltest specifies the total number of tests performed to obtain the list
of peaks. It should be larger than the largest number of peaks in A and B.
100 is too small. Thanks!

Best regards,

Julie


On 6/12/10 9:04 PM, "Noah Dowell" <noahd at ucla.edu> wrote:

> 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
>> 
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