Hello everyone,
I have some chicken ChIP-seq Solexa data, and I'm using chipseq package in the analysis. I'm having some problems with the diffPeakSummary -command, as it gives an error message: > peakSummary <- diffPeakSummary(ext, ext5, chrom.lens=chromlens, lower=8) Error in coverage.normargWidth(width, length(x)) : 'width' must be NULL or a single non-negative integer ext and ext5 have been produced with extendReads -command: > ext5 <- extendReads(faln5, seqLen=150) and chromlens is from the BSgenome.Ggallus.UCSC.galGal3 -package: > chromlens <- seqlengths(Ggallus) Any suggestions what could be the matter here? > sessionInfo() R version 2.10.0 Under development (unstable) (2009-08-23 r49375) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] chipseq_0.1.24 ShortRead_1.3.29 lattice_0.17-25 BSgenome_1.13.10 [5] Biostrings_2.13.34 IRanges_1.3.65 loaded via a namespace (and not attached): [1] Biobase_2.5.5 grid_2.10.0 hwriter_1.1 tools_2.10.0 Best regards, Sini -- Sini Junttila, MSc Turku Centre for Biotechnology Biocity, 5th floor Tykistökatu 6 20521 Turku Finland phone: +358 2 333 8041 fax: +358 2 333 8000 -- Sini Junttila, MSc Turku Centre for Biotechnology Biocity, 5th floor Tykistökatu 6 20521 Turku Finland phone: +358 2 333 8041 fax: +358 2 333 8000 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
