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Hi Donna, Donna Toleno wrote: > Hello, > > I have a few general questions about custom CDFs. I believe that I > have created a custom cdf environment by removing specific probes from > the current environment. > > I did so using a previous post > > http://article.gmane.org/gmane.science.biology.informatics.conductor /4258/match= > > > I can see that an affybatch object reflects > the modification of the cdf. My problem is that I don't understand how > to save this environment for future use. In fact I do not have a cdf > file for the cdf that I have created. Not sure what you mean by a cdf file. The environment you have created is sitting in your .GlobalEnv, which is really just your R workspace. If you quit R and save the workspace, then the environment will be there when you restart R in that directory (or restart R elsewhere, and then load() that workspace). This is the easiest way to save things. You could also make a package containing the environment, but that will take more work. If you really want to do this, take a look at the make.cdf.package() function in makecdfenv. You won't be able to use this function directly -- instead you will have to run the relevant portions (probably from 'symbols' on down, although I would have to try myself to know for sure). Best, Jim > > > when I do this: > newcdf <- wrapCdfEnvAffy(hgu133plus2cdf,1164,1164,"hgu133plus2cdf") > > I get an error > Error in as.environment(from) : invalid object for 'as.environment' > > The wrapCdfEnvAffy function creates a CdfEnvAffy object and then seems > to work OK until it gets to: > > valid <- validCdfEnvAffy(object, verbose = verbose) > > > The following is the result of: print (object) > > I believe it is the - in HG-U133_Plus_2 which causes the object to be > invalid. I am not sure what to do to get around this problem. I read a few > of the tutorials on the subject but I must be missing the answer. > > Any ideas would be appreciated. > > > An object of class "CdfEnvAffy" > Slot "envir": > <environment: 0x112e3ab8=""> > > Slot "envName": > [1] "HG-U133_Plus_2" > > Slot "index2xy": > function (object, i) > { > indices2xy(i, nr = object at nrow) - getOption("BioC")$affy$xy.offset > } > > Slot "xy2index": > function (object, x, y) > { > o <- getOption("BioC")$affy$xy.offset > xy2indices(x + o, y + o, nr = object at nrow) > } > > Slot "nrow": > [1] 1164 > > Slot "ncol": > [1] 1164 > > Slot "probeTypes": > [1] "pm" "mm" > > Slot "chipType": > [1] "HG-U133_Plus_2" > > > Thanks for reading. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623