Thanks, Michael.
In the ChipSeq vignette, it loads up 3 libraries, one is GenomicFeatures.Mmusculus.UCSC.mm9 Here is the output when I ran the example code: > example(diffPeakSummary) dffPkS> data(cstest) dffPkS> library(BSgenome.Mmusculus.UCSC.mm9) dffPkS> mouse.chromlens <- seqlengths(Mmusculus) dffPkS> ## extend reads, generate peak summary dffPkS> extRanges <- gdapply(cstest, extendReads, seqLen = 200) Error in X[[i]] : this S4 class is not subsettable Error in gdapply(X[[i]], FUN, ...) : error in evaluating the argument 'X' in selecting a method for function 'gdapply' > cstest An object of class ?GenomeDataList? Slot "annotation": Error in slot(object, what) : no slot of name "annotation" for this object of class "GenomeDataList" > "cstest" output is quite different from the vignette, so I assume GenomicFeatures.Mmusculus.UCSC.mm9 is required. -Kunbin From: Michael Lawrence [mailto:[email protected]] Sent: Monday, April 05, 2010 3:49 PM To: Kunbin Qu Cc: [email protected] Subject: Re: [Bioc-sig-seq] example(diffPeakSummary) in chipseq The example code (in svn at least) looks like it needs BSgenome.Mmusculus.UCSC.mm9, not GenomicFeatures. Maybe you're talking about the contextDistribution example, which could be considered deprecated/obsolete, until I figure out how chipseq should interact with the new generation of GenomicFeatures. Michael On Mon, Apr 5, 2010 at 3:38 PM, Kunbin Qu <[email protected]> wrote: Hi, I was trying to run the diffPeakSummary example code in chipseq. It needs to install GenomicFeatures.Mmusculus.UCSC.mm9. When I tried to install it, it gave the following error messages. Please help, thanks. -Kunbin > install.packages("/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar .gz", type="source") inferring 'repos = NULL' from the file name * Installing *source* package ?GenomicFeatures.Mmusculus.UCSC.mm9? ... ** R ** inst ** preparing package for lazy loading Loading required package: rtracklayer Loading required package: RCurl Loading required package: bitops Warning: Multiple methods tables found for 'duplicated' Warning: Multiple methods tables found for 'unique' Warning: Multiple methods tables found for 'sort' Warning: Multiple methods tables found for 'rank' Warning in namespaceImportFrom(self, asNamespace(ns)) : replacing previous import: .__C__Dups Warning in namespaceImportFrom(self, asNamespace(ns)) : replacing previous import: match Warning in namespaceImportFrom(self, asNamespace(ns)) : replacing previous import: summary Warning in namespaceImportFrom(self, asNamespace(ns)) : replacing previous import: .__C__Dups Warning in namespaceImportFrom(self, asNamespace(ns)) : replacing previous import: match ** help *** installing help indices >>> Building/Updating help pages for package 'GenomicFeatures.Mmusculus.UCSC.mm9' Formats: text html latex example ******* Syntax error: \enumerate in /----- A data frame with 16026 observations on the following 4 variables. \enumeratenormal-bracket12bracket-normal\----- ERROR: building help failed for package ?GenomicFeatures.Mmusculus.UCSC.mm9? * Removing ?/mnt/opt/R/R-2.9.2/x86_64-unknown-linux-gnu/lib64/R/library/GenomicFeat ures.Mmusculus.UCSC.mm9? Warning message: In install.packages("/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar .gz", : installation of package '/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar.gz' had non-zero exit status > sessionInfo() R version 2.9.2 (2009-08-24) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME= C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI ON=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Mmusculus.UCSC.mm9_1.3.13 chipseq_0.2.1 [3] ShortRead_1.2.1 lattice_0.17-26 [5] BSgenome_1.12.5 Biostrings_2.12.10 [7] IRanges_1.4.16 loaded via a namespace (and not attached): [1] Biobase_2.4.1 grid_2.9.2 hwriter_1.2 tools_2.9.2 > ______________________________________________________________________ The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. 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