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

[Patrick Aboyoun]

P. Terry,
The sequence infrastructure has been rapidly changing and it looks like 
you have incompatible packages in your snapshot. Updating your packages via

source("http://bioconductor.org/biocLite.R")
update.packages(repos = biocinstallRepos())

should do the trick.


Patrick


pterry at huskers.unl.edu wrote:
> 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)
> 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] 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?
>
> Thanks,
> P. Terry
> pterry at huskers.unl.edu
>
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