[Bioc-sig-seq] (no subject)

Sini Junttila sjunttil at btk.fi
Fri Sep 4 12:10:36 CEST 2009

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)

 [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

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 Junttila, MSc

Turku Centre for Biotechnology
Biocity, 5th floor
Tykistökatu 6
20521 Turku

phone: +358 2 333 8041
fax:   +358 2 333 8000

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