[BioC] oligo - copying V1Overview vigenette

[Benilton Carvalho]

Hi Lavinia,

thanks for the report, I'll have this fixed ASAP.

benilton

On 10 August 2010 03:32, Lavinia Gordon <lavinia.gordon at mcri.edu.au> wrote:
> Dear Bioconductors,
>
> I am just looking through one of the vignettes with the /oligo/ package
> (V1Overview.pdf).
> I have downloaded the test data from the Affymetrix link and am
> following the commands in the pdf:
>
> library(pd.hg.u95a)
> library(oligo)
> celfiles <- list.celfiles(getwd())
> affyExpressionFS <- read.celfiles(celfiles)
>  > class(affyExpressionFS)
> [1] "ExpressionFeatureSet"
> attr(,"package")
> [1] "oligoClasses"
>
> but then I get to:
>  > pmSeq <- pmSequence(affyExpressionFS)
> Warning message:
> In .local(object, ...) :
>   pmSequence.rda file is not available for this pdInfo pkg.
>
>  > pmSeq
> NULL
>
> pmSequence.rda is available, in Rdata.zip in
> R\R-2.11.0\library\pd.hg.u95a\data.  Any ideas how I can get R to
> realise that it is available?
>
> With thanks for your time,
>
> Lavinia Gordon.
>
>  > sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_Australia.1252
> LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pd.hg.u95a_0.99.0   oligo_1.12.2        oligoClasses_1.10.0
> Biobase_2.8.0       RSQLite_0.9-2       DBI_0.2-5
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.20.0     affyio_1.16.0         Biostrings_2.16.4
> IRanges_1.6.6         preprocessCore_1.10.0
> [6] splines_2.11.0        tools_2.11.0
>
> --
> Senior Bioinformatics Officer
> Murdoch Childrens Research Institute
> Royal Children's Hospital
> Flemington Road
> Parkville
> Victoria 3052
> Australia
> www.mcri.edu.au
>
>
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>
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