more question about makeVennDiagram
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
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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 [[alternative HTML version deleted]]
GO ChIPpeakAnno GO ChIPpeakAnno • 787 views
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xyang2 ▴ 120
@xyang2-4387
Last seen 11 months ago
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") 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 > > > [[alternative HTML version deleted]]
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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 [[alternative HTML version deleted]]
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Julie Zhu ★ 4.3k
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Holly, Looks like you created your peaks without assigning names for each range. The helper function BED2RangedData or GFF2RangedData automatically does that for you. The makeVennDiagram in ChIPpeakAnno 2.4 version assumes the RangedData has names. This assumption has been removed in ChIPpeakAnno dev 2.5.10 which you can download at http://bioconductor.org/packages/devel/bioc/html/ChIPpeakAnno.html. Alternatively, you can add names to your RangedData by using the above helper functions or using the code below before calling makeVennDiagram. rownames(Peaks_A)=1:dim(Peaks_A)[1] rownames(Peaks_B)=1:dim(Peaks_B)[1] Please let me know if it works out for you. Best regards, Julie On 8/1/12 11:45 AM, "Holly" <xyang2@uchicago.edu> wrote: Julie, Yes, the following example runs well. I attached my two peaks. Thanks a lot. Holly > peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), + end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), + space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) > peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260), + end = c(967869, 2011108, 2496920, 3076166, 3123470), + names = c("t1", "t2", "t3", "t4", "t5")), + space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a")) > makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1", "TF2"), + totalTest=100) $p.value [1] 6.184292e-05 $vennCounts TF1 TF2 Counts [1,] 0 0 95 [2,] 0 1 2 [3,] 1 0 0 [4,] 1 1 3 attr(,"class") [1] "VennCounts" Warning message: In findOverlappingPeaks(Peaks[[1]], Peaks[[2]], NameOfPeaks1 = NameOfPeaks[1], : Please use select instead of multiple! On 8/1/2012 8:32 AM, Zhu, Lihua (Julie) wrote: Re: more question about makeVennDiagram 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/window s/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 [[alternative HTML version deleted]]
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Julie, Yes, it works now. Thanks a lot, Holly On 8/1/2012 9:33 AM, Zhu, Lihua (Julie) wrote: > Re: more question about makeVennDiagram Holly, > > Looks like you created your peaks without assigning names for each > range. The helper function BED2RangedData or GFF2RangedData > automatically does that for you. The makeVennDiagram in ChIPpeakAnno > 2.4 version assumes the RangedData has names. This assumption has been > removed in ChIPpeakAnno dev 2.5.10 which you can download at > http://bioconductor.org/packages/devel/bioc/html/ChIPpeakAnno.html. > Alternatively, you can add names to your RangedData by using the above > helper functions or using the code below before calling makeVennDiagram. > > rownames(Peaks_A)=1:dim(Peaks_A)[1] > rownames(Peaks_B)=1:dim(Peaks_B)[1] > > Please let me know if it works out for you. > > Best regards, > > Julie > > > > On 8/1/12 11:45 AM, "Holly" <xyang2@uchicago.edu> wrote: > > > Julie, > Yes, the following example runs well. I attached my two peaks. > Thanks a lot. > Holly > > > peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), > + end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", > "Site3")), > + space = c("1", "2", "3"), > strand=as.integer(1),feature=c("a","b","f")) > > peaks2 = RangedData(IRanges(start = c(967659, > 2010898,2496700,3075866,3123260), > + end = c(967869, 2011108, 2496920, 3076166, 3123470), > + names = c("t1", "t2", "t3", "t4", "t5")), > + space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), > feature=c("a","b","c","d","a")) > > makeVennDiagram(RangedDataList(peaks1,peaks2), > NameOfPeaks=c("TF1", "TF2"), > + totalTest=100) > $p.value > [1] 6.184292e-05 > > $vennCounts > TF1 TF2 Counts > [1,] 0 0 95 > [2,] 0 1 2 > [3,] 1 0 0 > [4,] 1 1 3 > attr(,"class") > [1] "VennCounts" > > Warning message: > In findOverlappingPeaks(Peaks[[1]], Peaks[[2]], NameOfPeaks1 = > NameOfPeaks[1], : > Please use select instead of multiple! > > > > > On 8/1/2012 8:32 AM, Zhu, Lihua (Julie) wrote: > > > Re: more question about makeVennDiagram 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/wind ows/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 > > > > > > > > > > > > > [[alternative HTML version deleted]]
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