So, if none of the stopifnot() tests complaints, then it might be that
the CDF file might be corrupt or incomplete. Compare with the file
size and checksum that I get:
> library("aroma.affymetrix");
> pathname <-
> "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
> df <- GenericDataFile(pathname);
> df
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full
Full name: GenomeWideSNP_6,Full
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf
File size: 470.44 MB (493291745 bytes)
RAM: 0.00 MB
> getChecksum(df)
[1] "3fbe0f6e7c8a346105238a3f3d10d4ec"
/Henrik
On Wed, Sep 2, 2009 at 12:19 AM, JeromeW<jerome.woj...@gmail.com> wrote:
>
> Hi all
>
> I reply in this thread because I also have the "could not locate a
> file" problem which I cannot solve.
>
> My code:
> setwd("/x05/people/m140932/eclipse/workspace/CNV"); # here I set the
> working directory
> library("aroma.affymetrix");
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
> options(digits=4);
> stopifnot(isDirectory("annotationData"));
> stopifnot(isDirectory("annotationData/chipTypes"));
> stopifnot(isDirectory("annotationData/chipTypes/GenomeWideSNP_6"));
> stopifnot(isFile("annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,Full.cdf"));
> cdf <- AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags="Full");
>
> My paths and files:
>>pwd
> /x05/people/m140932/eclipse/workspace/CNV/annotationData/chipTypes/
> GenomeWideSNP_6
>>ll
> total 673949
> -rw-r--r-- 1 scicomp 493291745 2009-09-01 16:49
> GenomeWideSNP_6,Full.cdf
> -rw-r--r-- 1 scicomp 7526454 2009-09-02 07:54
> GenomeWideSNP_6,Full,na26,HB20080722.ufl
> -rw-r--r-- 1 scicomp 9407937 2009-09-02 07:55
> GenomeWideSNP_6,Full,na26,HB20080821.ugp
> -rw-r--r-- 1 scicomp 179217531 2009-09-02 08:03
> GenomeWideSNP_6,HB20080710.acs
>
> I checked many times the paths and filenames but cannot see the error.
> I still get the following error message:
> Error in list(`AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags =
> "Full")` = <environment>, :
> [2009-09-02 09:09:17] Exception: Could not locate a file for this chip
> type: GemomeWideSNP_6,Full
> at throw(Exception(...))
> at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipT
> at throw("Could not locate a file for this chip type: ", paste(c
> (chipType, tag
> at method(static, ...)
> at AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags = "Full")
>
> I am using R2.9.1 on Linux (with the Eclipse StatET plug-in).
>
> Thanks for your help
> cheers
> Jerome
>
> >
>
--~--~---------~--~----~------------~-------~--~----~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
