Summing Views on coverage by base
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@sean-davis-490
Last seen 4 months ago
United States
I have a set of Views of equal width (think upstream of tss) and want to sum each base across those views. I can extract each view as an integer vector and create a matrix, but this matrix can get pretty large. I'm missing the skills with SimpleRleViewsList, though, to work directly on at object. Any suggestions? Thanks, Sean > sessionInfo() R Under development (unstable) (2012-01-19 r58141) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.7.30 IRanges_1.13.28 BiocGenerics_0.1.12 loaded via a namespace (and not attached): [1] stats4_2.15.0 tools_2.15.0
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@herve-pages-1542
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Seattle, WA, United States
Hi Sean, On 03/20/2012 01:14 PM, Sean Davis wrote: > I have a set of Views of equal width (think upstream of tss) and want > to sum each base across those views. I can extract each view as an > integer vector and create a matrix, but this matrix can get pretty > large. I'm missing the skills with SimpleRleViewsList, though, to > work directly on at object. Any suggestions? > subject <- Rle(rep(c(0L, 1L, 3L, 2L, 18L, 0L), c(3,2,1,5,2,4))) > myViews <- Views(subject, start=4:11, width=5) > myViews Views on a 17-length Rle subject views: start end width [1] 4 8 5 [1 1 3 2 2] [2] 5 9 5 [1 3 2 2 2] [3] 6 10 5 [3 2 2 2 2] [4] 7 11 5 [2 2 2 2 2] [5] 8 12 5 [ 2 2 2 2 18] [6] 9 13 5 [ 2 2 2 18 18] [7] 10 14 5 [ 2 2 18 18 0] [8] 11 15 5 [ 2 18 18 0 0] This maybe would be fast enough if you don't have too many columns: viewColSums <- function(x) { sapply(seq_len(width(x)[1L]), function(i) sum(subject[start(x)+i-1L])) } > viewColSums(myViews) [1] 15 32 49 46 44 Then if your SimpleRleViewsList object is not too long (1 elt per chromosome?), you can sapply( , viewColSums) on it. Maybe we should make viewColSums the "colSums" method for RleViews objects? (and eventually implement it in C?) Cheers, H. > > Thanks, > Sean > >> sessionInfo() > R Under development (unstable) (2012-01-19 r58141) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicRanges_1.7.30 IRanges_1.13.28 BiocGenerics_0.1.12 > > loaded via a namespace (and not attached): > [1] stats4_2.15.0 tools_2.15.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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On 03/20/2012 01:40 PM, Hervé Pagès wrote: [...] > This maybe would be fast enough if you don't have too many columns: > > viewColSums <- function(x) > { > sapply(seq_len(width(x)[1L]), > function(i) > sum(subject[start(x)+i-1L])) sum(subject(x)[start(x)+i-1L])) of course... H.
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On 03/20/2012 01:40 PM, Hervé Pagès wrote: > Hi Sean, > > On 03/20/2012 01:14 PM, Sean Davis wrote: >> I have a set of Views of equal width (think upstream of tss) and want >> to sum each base across those views. I can extract each view as an >> integer vector and create a matrix, but this matrix can get pretty >> large. I'm missing the skills with SimpleRleViewsList, though, to >> work directly on at object. Any suggestions? > > > subject <- Rle(rep(c(0L, 1L, 3L, 2L, 18L, 0L), c(3,2,1,5,2,4))) > > myViews <- Views(subject, start=4:11, width=5) > > myViews > Views on a 17-length Rle subject > > views: > start end width > [1] 4 8 5 [1 1 3 2 2] > [2] 5 9 5 [1 3 2 2 2] > [3] 6 10 5 [3 2 2 2 2] > [4] 7 11 5 [2 2 2 2 2] > [5] 8 12 5 [ 2 2 2 2 18] > [6] 9 13 5 [ 2 2 2 18 18] > [7] 10 14 5 [ 2 2 18 18 0] > [8] 11 15 5 [ 2 18 18 0 0] > > This maybe would be fast enough if you don't have too many columns: > > viewColSums <- function(x) > { > sapply(seq_len(width(x)[1L]), > function(i) > sum(subject[start(x)+i-1L])) > } > > > viewColSums(myViews) > [1] 15 32 49 46 44 Reduce("+", myViews) > > Then if your SimpleRleViewsList object is not too long (1 elt per > chromosome?), you can sapply( , viewColSums) on it. > > Maybe we should make viewColSums the "colSums" method for RleViews > objects? (and eventually implement it in C?) > > Cheers, > H. > >> >> Thanks, >> Sean >> >>> sessionInfo() >> R Under development (unstable) (2012-01-19 r58141) >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GenomicRanges_1.7.30 IRanges_1.13.28 BiocGenerics_0.1.12 >> >> loaded via a namespace (and not attached): >> [1] stats4_2.15.0 tools_2.15.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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2012/3/20 Martin Morgan <mtmorgan at="" fhcrc.org="">: > On 03/20/2012 01:40 PM, Hervé Pagès wrote: >> Hi Sean, >> >> On 03/20/2012 01:14 PM, Sean Davis wrote: >>> I have a set of Views of equal width (think upstream of tss) and want >>> to sum each base across those views. I can extract each view as an >>> integer vector and create a matrix, but this matrix can get pretty >>> large. I'm missing the skills with SimpleRleViewsList, though, to >>> work directly on at object. Any suggestions? >> >> ?> subject <- Rle(rep(c(0L, 1L, 3L, 2L, 18L, 0L), c(3,2,1,5,2,4))) >> ?> myViews <- Views(subject, start=4:11, width=5) >> ?> myViews >> Views on a 17-length Rle subject >> >> views: >> start end width >> [1] 4 8 5 [1 1 3 2 2] >> [2] 5 9 5 [1 3 2 2 2] >> [3] 6 10 5 [3 2 2 2 2] >> [4] 7 11 5 [2 2 2 2 2] >> [5] 8 12 5 [ 2 2 2 2 18] >> [6] 9 13 5 [ 2 2 2 18 18] >> [7] 10 14 5 [ 2 2 18 18 0] >> [8] 11 15 5 [ 2 18 18 0 0] >> >> This maybe would be fast enough if you don't have too many columns: >> >> viewColSums <- function(x) >> { >> sapply(seq_len(width(x)[1L]), >> function(i) >> sum(subject[start(x)+i-1L])) >> } >> >> ?> viewColSums(myViews) >> [1] 15 32 49 46 44 > > > Reduce("+", myViews) Nice. Sean >> >> Then if your SimpleRleViewsList object is not too long (1 elt per >> chromosome?), you can sapply( , viewColSums) on it. >> >> Maybe we should make viewColSums the "colSums" method for RleViews >> objects? (and eventually implement it in C?) >> >> Cheers, >> H. >> >>> >>> Thanks, >>> Sean >>> >>>> sessionInfo() >>> R Under development (unstable) (2012-01-19 r58141) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] GenomicRanges_1.7.30 IRanges_1.13.28 BiocGenerics_0.1.12 >>> >>> loaded via a namespace (and not attached): >>> [1] stats4_2.15.0 tools_2.15.0 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793
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On 03/20/2012 03:10 PM, Sean Davis wrote: > 2012/3/20 Martin Morgan<mtmorgan at="" fhcrc.org="">: >> On 03/20/2012 01:40 PM, Hervé Pagès wrote: >>> Hi Sean, >>> >>> On 03/20/2012 01:14 PM, Sean Davis wrote: >>>> I have a set of Views of equal width (think upstream of tss) and want >>>> to sum each base across those views. I can extract each view as an >>>> integer vector and create a matrix, but this matrix can get pretty >>>> large. I'm missing the skills with SimpleRleViewsList, though, to >>>> work directly on at object. Any suggestions? >>> >>> > subject<- Rle(rep(c(0L, 1L, 3L, 2L, 18L, 0L), c(3,2,1,5,2,4))) >>> > myViews<- Views(subject, start=4:11, width=5) >>> > myViews >>> Views on a 17-length Rle subject >>> >>> views: >>> start end width >>> [1] 4 8 5 [1 1 3 2 2] >>> [2] 5 9 5 [1 3 2 2 2] >>> [3] 6 10 5 [3 2 2 2 2] >>> [4] 7 11 5 [2 2 2 2 2] >>> [5] 8 12 5 [ 2 2 2 2 18] >>> [6] 9 13 5 [ 2 2 2 18 18] >>> [7] 10 14 5 [ 2 2 18 18 0] >>> [8] 11 15 5 [ 2 18 18 0 0] >>> >>> This maybe would be fast enough if you don't have too many columns: >>> >>> viewColSums<- function(x) >>> { >>> sapply(seq_len(width(x)[1L]), >>> function(i) >>> sum(subject[start(x)+i-1L])) >>> } >>> >>> > viewColSums(myViews) >>> [1] 15 32 49 46 44 >> >> >> Reduce("+", myViews) > > Nice. maybe too many class coercions in there, though Reduce(function(x, y) x + as.integer(y), myViews, 0L) which seems like a step or so back... Martin > > Sean > > >>> >>> Then if your SimpleRleViewsList object is not too long (1 elt per >>> chromosome?), you can sapply( , viewColSums) on it. >>> >>> Maybe we should make viewColSums the "colSums" method for RleViews >>> objects? (and eventually implement it in C?) >>> >>> Cheers, >>> H. >>> >>>> >>>> Thanks, >>>> Sean >>>> >>>>> sessionInfo() >>>> R Under development (unstable) (2012-01-19 r58141) >>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] GenomicRanges_1.7.30 IRanges_1.13.28 BiocGenerics_0.1.12 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] stats4_2.15.0 tools_2.15.0 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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On 03/20/2012 03:32 PM, Martin Morgan wrote: > On 03/20/2012 03:10 PM, Sean Davis wrote: >> 2012/3/20 Martin Morgan<mtmorgan at="" fhcrc.org="">: >>> On 03/20/2012 01:40 PM, Hervé Pagès wrote: >>>> Hi Sean, >>>> >>>> On 03/20/2012 01:14 PM, Sean Davis wrote: >>>>> I have a set of Views of equal width (think upstream of tss) and want >>>>> to sum each base across those views. I can extract each view as an >>>>> integer vector and create a matrix, but this matrix can get pretty >>>>> large. I'm missing the skills with SimpleRleViewsList, though, to >>>>> work directly on at object. Any suggestions? >>>> >>>> > subject<- Rle(rep(c(0L, 1L, 3L, 2L, 18L, 0L), c(3,2,1,5,2,4))) >>>> > myViews<- Views(subject, start=4:11, width=5) >>>> > myViews >>>> Views on a 17-length Rle subject >>>> >>>> views: >>>> start end width >>>> [1] 4 8 5 [1 1 3 2 2] >>>> [2] 5 9 5 [1 3 2 2 2] >>>> [3] 6 10 5 [3 2 2 2 2] >>>> [4] 7 11 5 [2 2 2 2 2] >>>> [5] 8 12 5 [ 2 2 2 2 18] >>>> [6] 9 13 5 [ 2 2 2 18 18] >>>> [7] 10 14 5 [ 2 2 18 18 0] >>>> [8] 11 15 5 [ 2 18 18 0 0] >>>> >>>> This maybe would be fast enough if you don't have too many columns: >>>> >>>> viewColSums<- function(x) >>>> { >>>> sapply(seq_len(width(x)[1L]), >>>> function(i) >>>> sum(subject[start(x)+i-1L])) >>>> } >>>> >>>> > viewColSums(myViews) >>>> [1] 15 32 49 46 44 >>> >>> >>> Reduce("+", myViews) >> >> Nice. > > maybe too many class coercions in there, though > > Reduce(function(x, y) x + as.integer(y), myViews, 0L) > > which seems like a step or so back... FWIW, the main difference between using viewColSums() and Reduce() is that the former loops on the columns while the latter loops on the rows. So what's best for you depends on the geometry of your Views object. Cheers, H. > > Martin > >> >> Sean >> >> >>>> >>>> Then if your SimpleRleViewsList object is not too long (1 elt per >>>> chromosome?), you can sapply( , viewColSums) on it. >>>> >>>> Maybe we should make viewColSums the "colSums" method for RleViews >>>> objects? (and eventually implement it in C?) >>>> >>>> Cheers, >>>> H. >>>> >>>>> >>>>> Thanks, >>>>> Sean >>>>> >>>>>> sessionInfo() >>>>> R Under development (unstable) (2012-01-19 r58141) >>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>>> >>>>> locale: >>>>> [1] C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] GenomicRanges_1.7.30 IRanges_1.13.28 BiocGenerics_0.1.12 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] stats4_2.15.0 tools_2.15.0 >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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On Tue, Mar 20, 2012 at 6:32 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 03/20/2012 03:10 PM, Sean Davis wrote: >> >> 2012/3/20 Martin Morgan<mtmorgan at="" fhcrc.org="">: >>> >>> On 03/20/2012 01:40 PM, Hervé Pagès wrote: >>>> >>>> Hi Sean, >>>> >>>> On 03/20/2012 01:14 PM, Sean Davis wrote: >>>>> >>>>> I have a set of Views of equal width (think upstream of tss) and want >>>>> to sum each base across those views. I can extract each view as an >>>>> integer vector and create a matrix, but this matrix can get pretty >>>>> large. I'm missing the skills with SimpleRleViewsList, though, to >>>>> work directly on at object. Any suggestions? >>>> >>>> >>>> ?> ?subject<- Rle(rep(c(0L, 1L, 3L, 2L, 18L, 0L), c(3,2,1,5,2,4))) >>>> ?> ?myViews<- Views(subject, start=4:11, width=5) >>>> ?> ?myViews >>>> Views on a 17-length Rle subject >>>> >>>> views: >>>> start end width >>>> [1] 4 8 5 [1 1 3 2 2] >>>> [2] 5 9 5 [1 3 2 2 2] >>>> [3] 6 10 5 [3 2 2 2 2] >>>> [4] 7 11 5 [2 2 2 2 2] >>>> [5] 8 12 5 [ 2 2 2 2 18] >>>> [6] 9 13 5 [ 2 2 2 18 18] >>>> [7] 10 14 5 [ 2 2 18 18 0] >>>> [8] 11 15 5 [ 2 18 18 0 0] >>>> >>>> This maybe would be fast enough if you don't have too many columns: >>>> >>>> viewColSums<- function(x) >>>> { >>>> sapply(seq_len(width(x)[1L]), >>>> function(i) >>>> sum(subject[start(x)+i-1L])) >>>> } >>>> >>>> ?> ?viewColSums(myViews) >>>> [1] 15 32 49 46 44 >>> >>> >>> >>> Reduce("+", myViews) >> >> >> Nice. > > > maybe too many class coercions in there, though > > ?Reduce(function(x, y) x + as.integer(y), myViews, 0L) > > which ?seems like a step or so back... But 30% faster. Thanks again. Sean >> >> Sean >> >> >>>> >>>> Then if your SimpleRleViewsList object is not too long (1 elt per >>>> chromosome?), you can sapply( , viewColSums) on it. >>>> >>>> Maybe we should make viewColSums the "colSums" method for RleViews >>>> objects? (and eventually implement it in C?) >>>> >>>> Cheers, >>>> H. >>>> >>>>> >>>>> Thanks, >>>>> Sean >>>>> >>>>>> sessionInfo() >>>>> >>>>> R Under development (unstable) (2012-01-19 r58141) >>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>>> >>>>> locale: >>>>> [1] C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] GenomicRanges_1.7.30 IRanges_1.13.28 BiocGenerics_0.1.12 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] stats4_2.15.0 tools_2.15.0 >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 > > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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The C implementation would be highly appreciated. I currently do this operation with tools that are not R/Bioconductor-based for performance reasons. Thank you, Ivan Ivan Gregoretti, PhD 2012/3/20 Hervé Pagès <hpages at="" fhcrc.org="">: > Hi Sean, > > > On 03/20/2012 01:14 PM, Sean Davis wrote: >> >> I have a set of Views of equal width (think upstream of tss) and want >> to sum each base across those views. ?I can extract each view as an >> integer vector and create a matrix, but this matrix can get pretty >> large. ?I'm missing the skills with SimpleRleViewsList, though, to >> work directly on at object. ?Any suggestions? > > >> subject <- Rle(rep(c(0L, 1L, 3L, 2L, 18L, 0L), c(3,2,1,5,2,4))) >> myViews <- Views(subject, start=4:11, width=5) >> myViews > Views on a 17-length Rle subject > > views: > ? ?start end width > [1] ? ? 4 ? 8 ? ? 5 [1 1 3 2 2] > [2] ? ? 5 ? 9 ? ? 5 [1 3 2 2 2] > [3] ? ? 6 ?10 ? ? 5 [3 2 2 2 2] > [4] ? ? 7 ?11 ? ? 5 [2 2 2 2 2] > [5] ? ? 8 ?12 ? ? 5 [ 2 ?2 ?2 ?2 18] > [6] ? ? 9 ?13 ? ? 5 [ 2 ?2 ?2 18 18] > [7] ? ?10 ?14 ? ? 5 [ 2 ?2 18 18 ?0] > [8] ? ?11 ?15 ? ? 5 [ 2 18 18 ?0 ?0] > > This maybe would be fast enough if you don't have too many columns: > > viewColSums <- function(x) > { > ? ?sapply(seq_len(width(x)[1L]), > ? ? ? ? ? function(i) > ? ? ? ? ? ? ? sum(subject[start(x)+i-1L])) > } > >> viewColSums(myViews) > [1] 15 32 49 46 44 > > Then if your SimpleRleViewsList object is not too long (1 elt per > chromosome?), you can sapply( , viewColSums) on it. > > Maybe we should make viewColSums the "colSums" method for RleViews > objects? (and eventually implement it in C?) > > Cheers, > H. > > >> >> Thanks, >> Sean >> >>> sessionInfo() >> >> R Under development (unstable) (2012-01-19 r58141) >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] GenomicRanges_1.7.30 IRanges_1.13.28 ? ? ?BiocGenerics_0.1.12 >> >> loaded via a namespace (and not attached): >> [1] stats4_2.15.0 tools_2.15.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: ?(206) 667-5791 > Fax: ? ?(206) 667-1319 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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