
Looks like you don't have permission to write to:

/home/server/uid/R_LIBS/

check with your admin or do a local installation as described at:

http://www.biostat.wisc.edu/~kbroman/Rintro/

(very bottom of the page)

As for the pkgname... the problem is that the CEL file points to At35b_MR_v04 and your BPMAP was named At35b_MR_v04-2_TIGRv5.bpmap

try the following, after installing the package you created with makePlatformDesign:

test <- read.celfiles("T1_R1.cel", pkgname="pd.at35b.mr.v04.2.tigrv5")

b


-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Gayla Olbricht
Sent: Mon 10/29/2007 1:48 PM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] makePDpackage: Problem loading PD package in oligo:read.celfiles function
 
Hello,

I am trying to read and work with data from an Affymetrix tiling array.  (And appreciate the previous posts for working with such data)!  I am using the packages "makePlatformDesign" and "oligo".  

I have successfully used the makePDpackage function to create the needed package (pd.at35b.mr.v04.2.tigrv5)
makePDpackage("At35b_MR_v04-2_TIGRv5.bpmap", type="tiling", manufacturer="affymetrix")

However, when using oligo to read my CEL files, I run into a problem.
test<-read.celfiles("T1_R1.cel")

I get the following Error message:
Loading required package: pd.at35b.mr.v04
Error: invalid version specification

I've also tried installing the package directly
install.packages("pd.at35b.mr.v04.2.tigrv5", repos=NULL)

And get the following errors:
Warning in install.packages("/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5",  :
  argument 'lib' is missing: using '/home/server/uid/R_LIBS'
ERROR: cannot install to srcdir
Warning message:
In install.packages("/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5",  :
  installation of package '/home/server/uid/R_LIBS/pd.at35b.mr.v04.2.tigrv5' had non-zero exit status

One final thing I did notice is the package created by makePlatformDesign is pd.at35b.mr.v04.2.tigrv5, which is slightly different than the package it tries to load under the read.celfiles function (pd.at35b.mr.v04).

Any ideas or suggestions for how I can use the package I created to read my cel files would be appreciated.  My sessionInfo() is pasted below.

Thank you,
-Gayla Olbricht


> sessionInfo()
R version 2.6.0 (2007-10-03) 
x86_64-redhat-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;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_IDENTIFICATION=C

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

other attached packages:
 [1] makePlatformDesign_1.2.0 affyio_1.6.1             oligo_1.2.1             
 [4] oligoClasses_1.0.3       affxparser_1.10.1        AnnotationDbi_1.0.6     
 [7] preprocessCore_1.0.0     RSQLite_0.6-3            DBI_0.2-4               
[10] Biobase_1.16.1          

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15


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