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

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