[BioC] Questions on getting information from affy's CEL, CDF or 1lq file s

Laurent Gautier laurent at cbs.dtu.dk
Thu Mar 13 04:31:19 MET 2003


On Wed, Mar 12, 2003 at 02:14:37PM -0800, Wang, Hui wrote:
> Hi,
> 
> I am trying to use read.affybatch, however encountering the below error. 
> 
> Since the cdf I was using doesnot belong to any of the standard ones, could
> that be the problem? If yes, how do I attach my own cdf? 
> 
> Thanks
> 
> -hui
> 
> 
> > cdf.env<-read.cdffile("test.CDF") 
> >read.affybatch("030228_01_GL.CEL",  "030228_02_GL.CEL")
> AffyBatch object
> size of arrays=712x712 features (7924 kb)
> Error in .local(object, ...) : Information about probe locations for test
> could not be found. Try downloading the testcdf package from
> http://www.bioconductor.org/data/cdfenvs/cdfenvs.html
> In addition: Warning message: 
> Incompatible phenoData object. Created a new one.
>  in: read.affybatch("030228_01_GL.CEL", "030228_02_GL.CEL") 
> cdf=test (0 affyids)
> number of samples=2
> Error in .local(object, ...) : Information about probe locations for test
> could not be found. Try downloading the testcdf package from
> http://www.bioconductor.org/data/cdfenvs/cdfenvs.html
> 
> 


Dear Hui,


The function 'read.cdffile' reads .CDF files, and store the results
in an object of class Cdf (doing 'help(read.cdffile)' tells it, and
even more, like to refer to the doc for 'Cdf' to know more).

The doc for read.affybatch leads to the one for AffyBatch, in which
I admit things could be clearer (you will however note that it points
to the vignette, in which things are (a bit) clear(er)).

The class 'Cdf' and the cdf environments are two different structures.

For what you seems wanting to do (just guessing), you may have to 
work with both structures at the same time. For example, the Cdf are
better for dealing with what exactly is on a Cdf. In your previous
post, the neat way to get 'non-control/non-qc' probes is probably to
use the fuction 'pmormm'. You may also want to generate cdfenvironments
a quick way. Check the function 'getLocationsData.Cdf' for that.


Hopin' it helps,



L.



(the environments could also have their own class soon (if no one is fast enough
 to stop me ;) ) 




-- 
--------------------------------------------------------------
currently at the National Yang-Ming University in Taipei, Taiwan
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent



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