Hi,

I am trying to use makePDpackage and oligo to process Nimblegen arrays,
but I get an error in read.xysfiles:
> test.exprs <- read.xysfiles(list.xysfiles(),pkg='pd.tr.am.tiling')
Loading required package: pd.tr.am.tiling
Error in geometry(get(pkgname)) : 
  no slot of name "geometry" for this object of class "platformDesign"

This error does not happen in R 2.5.1 with oligo 1.0.2-6  
I notice that other users have had the same error message:
http://article.gmane.org/gmane.science.biology.informatics.conductor/195
08/
https://stat.ethz.ch/pipermail/bioc-devel/attachments/20080715/df48e1ad/
attachment.pl
http://article.gmane.org/gmane.science.biology.informatics.conductor/192
51/

Unfortunately, they have not received help on this issue, but maybe
somebody could still help me?

All the best,
Mikko Arvas



Here is the whole set of commands:

First I make the PD package:
> library(makePlatformDesign)
>
makePDpackage("TR_AM_Tiling.ndf","13347602_532_pair.txt.xys",manufacture
r='nimblegen')
nimblegen expression 
The package will be called pd.tr.am.tiling 
Reading TR_AM_Tiling.ndf 
Assuming a simple design (NOT multiple-wells).
Creating package in /pd.tr.am.tiling 
[1] "pd.tr.am.tiling"

Then I install it:
# R CMD INSTALL pd.tr.am.tiling/
* Installing to library '/usr/local/lib64/R-2.8.0/lib64/R/library'
* Installing *source* package 'pd.tr.am.tiling' ...
** R
** data
** preparing package for lazy loading
** help
chmod: cannot access
`/usr/local/lib64/R-2.8.0/lib64/R/library/pd.tr.am.tiling/man/pd.tr.am.t
iling.Rd.gz': No such file or directory
 >>> Building/Updating help pages for package 'pd.tr.am.tiling'
     Formats: text html latex example 
** building package indices ...
Warning in max.default(numeric(0), na.rm = FALSE) :
  no non-missing arguments to max; returning -Inf
* DONE (pd.tr.am.tiling)

And try to read in xys files:
> test.exprs <- read.xysfiles(list.xysfiles(),pkg='pd.tr.am.tiling')
Loading required package: pd.tr.am.tiling
Error in geometry(get(pkgname)) : 
  no slot of name "geometry" for this object of class "platformDesign"

> sessionInfo()
R version 2.8.0 (2008-10-20) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
ON=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets

[8] methods   base     

other attached packages:
 [1] limma_2.16.2             pd.tr.am.tilingori_1.6.0
makePlatformDesign_1.6.0
 [4] oligo_1.6.0              oligoClasses_1.4.0       affxparser_1.14.0

 [7] AnnotationDbi_1.4.0      preprocessCore_1.4.0     RSQLite_0.7-1

[10] DBI_0.2-4                Biobase_2.2.0            affyio_1.10.0



Mikko Arvas
VTT Technical Research Centre of Finland
Protein Production Team
E-mail     mikko.arvas@vtt.fi
Phone    +385-(0)40-754 1857
Fax        +358-(0)20-722 7071
Address  Tietotie 2 
               PL 1000 
               02044 VTT
               Finland
Web pages:
VTT: www.vtt.fi
Protein Production:
http://www.vtt.fi/palvelut/cluster4/topic4_3/Proteiinin_tuotto.jsp



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