[Bioc-sig-seq] ChIP-seq readReads question

pterry at huskers.unl.edu pterry at huskers.unl.edu
Mon Sep 28 18:03:40 CEST 2009

Dear Bioc-sig-sequencing,

In lab 8 at BioC2009 on 07/28/09 (Some Basic ChIP-Seq Data Analysis) presented by D. Sarkar, I would like to be able to get Eland aligned data (from a *_export.txt file) into a data structure like the 'cstest' data on page 1 of that handout.  This so that I can run an analysis like the poisson distribution analysis on page 7 of the handout.

I tried the following:

> arabchr1test <- readReads(".", "s_8_export.txt", include = "chr1", simplify = TRUE)
Error in validObject(.Object) :
  invalid class "SRFilter" object: superclass "ANYTHING" not defined in the environment of the object's class
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-11 r49665)

 [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] GenomicFeatures_0.0.9 chipseq_0.1.26        ShortRead_1.3.34
[4] lattice_0.17-25       BSgenome_1.13.11      Biostrings_2.13.38
[7] IRanges_1.3.79

loaded via a namespace (and not attached):
[1] Biobase_2.5.6 grid_2.10.0   hwriter_1.1

Can you comment on how I might successfully proceed?

P. Terry
pterry at huskers.unl.edu

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