Entering edit mode
Lavinia Gordon
▴
480
@lavinia-gordon-2959
Last seen 10.3 years ago
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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