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@molgen.mpg.de] Sent: Wednesday, March 12, 2003 10:17 AM To: Wang, Hui Cc: boiconductor@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

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