Thanks for the quick response!
The reason behind this problem came from a project I am working on. I
want to analyze Affymetrix 250k_nsp data in R, but there is no
suitable annotation cdf package available. On this moment I am using
an alternative cdf package from the brainarray website (http://
brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/
entrezg.asp) annotated with the entrezg database. This package
however, has only 0.8% (2803) of the originally amount of over 3.2
million probes, so a lot of valuable data is lost that way. I will
show some of my code here:
>library(affy)
>library(limma)
>library(mapping250knsphsentrezgcdf)
>library(mapping250knsphsentrezg.db)
>library(mapping250knsphsentrezgprobe)
>setwd("/data/home/pavandervelden/Minor/Tumor")
>t250knsp <- ReadAffy(cdfname="mapping250knsphsentrezgcdf")
With 'ReadAffy' it is not possible to use a cdf file that is not
installed as a package, only cdf environments are allowed. There comes
the reason why I cannot use the cdf files provided by Affymetrix, when
I want to make a cdf environment with those cdf files I keep on
getting messages that it is not a real cdf file (CustomCDF package
from brainarray), or that it cannot be read the right way. Usage of
the 'pd.mapping250k.nsp' package is also not an option in this method.
Shortly said: I want to build an full annotation package set (cdf
package, probe package and .db package) with the original, untouched
data from Affymetrix and I hoped to create a cdf file that would be
accepted by the functions that were able to create a cdf environment
in R. Maybe that is possible wit the aroma package, but I did not find
out a way how. I think it is because it isn't a expression array, but
I hope i am wrong and that it IS possible.
I hope you can help me!
Kind regards,
Sake van Pelt
On 28 jan, 19:34, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi,
>
> before anything else, what are the problems you're experiencing with
> the official Affymetrix CDF file:
>
> > I know I can download a cdf file from the Affymetrix website, but that
> > file doesn't work for me..
>
> That CDF has been used for many year and yet I haven't heard anyone
> else having problems with it. There is probably a simple reason and
> solution for your problems. Let us know what's not working and we'll
> help you.
>
> About writeCdf(): writeCdf() is a cleanup version of community
> contributed pdInfo2Cdf() with the difference that writeCdf() is easier
> to use. I missed to flag it an early-beta version, because it hasn't
> undergone rigorous testing on multiple chip types; it [pdInfo2Cdf()]
> was original designed for expression arrays and has hence only been
> used/tested for such. My best guess is that the current code does not
> work SNP chips. I add it to the todo list.
>
> Hope this helps
>
> /Henrik
>
> On Fri, Jan 28, 2011 at 1:25 AM, Sake van Pelt
>
> <tlep.nav.eka...@gmail.com> wrote:
> > Hi all,
>
> > I'm trying to extract a cdf file from the R platform design package of
> > the Affymetrix 250k_Nsp array. I used the writeCdf.AffyGenePDInfo
> > function.
> > This is my code:
>
> >>library(aroma.affymetrix)
> >>library(pd.mapping250k.nsp)
> >>library(affxparser)
> >>library(pdInfoBuilder)
> >>writeCdf.AffyGenePDInfo(pd.mapping250k.nsp)
>
> > It starts very promising:
>
> > Generating CDF file from Platform Design (PD) package...
> > Platform Design (PD) package: pd.mapping250k.nsp
> > Output path: annotationData/chipTypes/Mapping250K_Nsp
> > Filename: Mapping250K_Nsp.cdf
> > Pathname to generated CDF: annotationData/chipTypes/Mapping250K_Nsp/
> > Mapping250K_Nsp.cdf
> > Chip type: Mapping250K_Nsp
> > Tags:
> > Chip type dimensions: 2560x2560
> > Total number of cells (probes): 6553600
> > Querying Platform Design database...
> > 'data.frame': 3221600 obs. of 7 variables:
> > $ fid : int 2566 2568 2570 2572 2574 2576 2578 2580 2582
> > 2584 ...
> > $ strand: int 0 1 1 0 1 0 0 0 0 0 ...
> > $ allele: int 0 0 1 0 1 0 0 0 0 1 ...
> > $ fsetid: int 258185 192040 236691 139532 24150 41056 185256
> > 133631 258800 234975 ...
> > $ pos : int 4 7 7 2 9 5 3 1 4 5 ...
> > $ x : int 5 7 9 11 13 15 17 19 21 23 ...
> > $ y : int 1 1 1 1 1 1 1 1 1 1 ...
> > Number of cells (probes) in PD database: 3221600 (49.16%) of 6553600
> > Querying Platform Design database...done
> > Creating list from query table...
> > Number of units: 262264
> > Average number of cells per units: 12.28
> > Creating list from query table...done
> > Setting up CDF tree structure...
> > Setting CDF header...
> > Setting CDF header...done
> > Setting up CDF units...
> > Number of units: 262264
>
> > But then I get the following message:
>
> > Error in order(u$atom) : argument 1 is not a vector
>
> >> sessionInfo()
> > R version 2.12.0 (2010-10-15)
> > Platform: x86_64-redhat-linux-gnu (64-bit)
>
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> > [9] LC_ADDRESS=C LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
>
> > other attached packages:
> > [1] pdInfoBuilder_1.14.1 pd.mapping250k.nsp_1.1.0
> > oligoClasses_1.12.2
> > [4] Biobase_2.10.0 RSQLite_0.9-4 DBI_0.2-5
> > [7] aroma.affymetrix_1.9.0 aroma.apd_0.1.7
> > affxparser_1.22.1
> > [10] R.huge_0.2.0 aroma.core_1.9.1
> > aroma.light_1.18.2
> > [13] matrixStats_0.2.2 R.rsp_0.4.1 R.cache_0.3.0
> > [16] R.filesets_0.9.1 digest_0.4.2 R.utils_1.6.0
> > [19] R.oo_1.7.4 oligo_1.14.0
> > R.methodsS3_1.2.1
>
> > loaded via a namespace (and not attached):
> > [1] affyio_1.18.0 Biostrings_2.18.2 IRanges_1.8.8
> > [4] preprocessCore_1.12.0 splines_2.12.0
>
> >> traceback()
> > No traceback available
>
> > I know I can download a cdf file from the Affymetrix website, but that
> > file doesn't work for me..
> > I hope someone can help me!
>
> > Kind regards,
>
> > Sake van Pelt
> > Graduating Bio-Informatics student at the University of Applied
> > Sciences in Leiden, Netherlands
>
> > --
> > 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 with websitehttp://www.aroma-project.org/.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
--
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 with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
