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

[Wang, Hui]

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




-----Original Message-----
From: Dennis Kostka [mailto:dennis.kostka at molgen.mpg.de] 
Sent: Wednesday, March 12, 2003 10:17 AM
To: Wang, Hui
Cc: boiconductor at stat.math.ethz.ch
Subject: Re: [BioC] Questions on getting information from affy's CEL, CDF or
1lq file s


On Wednesday 12 March 2003 18:28, Wang, Hui wrote:
> Greetings,
>
> I am exploring the affy packages and I have trouble to get information
> I need (part is because I am not so farmilar with the language and the 
> package). I have the following questions, your help will be really 
> appreciated.
>
>
> 1)how to get the coordinates of each probe intensities? For example,
> in the .CEL file, there is x, y and intensity columns corresponding to 
> each probes. I used read.celfile to read information. If there seems 
> no way to get the x, y columns which are the corrdinate of the probes 
> (there is no method provided from Class Cel). Are there other 
> functions to use?  Similar question to .CDF file.

for the CEL file coordinates:
i would calculate them from the the index of the expression slot of the 
AffyBatch object (call it abo) like this:
	i2xy <- function(i){cbind((i-1)%%nrow(abo) , (i-1)%/%ncol(abo))} so
that i2xy(a) should return the x and y coordinate of a (starting from 0 as 
in the CEL file). important is that a is the index of the intensity you're 
interested in, not hte intensity itself.  x and y might be swapped, but you 
could check that in the file.

> 2). How to extract non-control, non-qc probe information?

i.e. like in the bg.correct.mas function:
	pm.i <- unique(unlist(indexProbes(abo,"pm")))
returns the indices of perfect match probes, where abo is the AffyBatch 
object. for the mismatches you just have to exchange "pm" to "mm".

> 3) for many of the functions listed under affy package, there is no
> help file. For a simple example, read.affybatch, or write.celfile etc. 
> are there other place to look?

typing 
	>?read.affybatch 
works at the installation here. i don't know about help files, but if there
is 
one called something like "AffyBatch-class.something" that's where i'd look.

dennis