Hi Donna, Donna wrote: > > James MacDonald <jmacdon at="" ...=""> writes: > >> Hi Donna, >> >> See the function posted by Jenny Drnevich about half way down this post: >> >> > http://article.gmane.org/gmane.science.biology.informatics.conductor /9887/match=probe+mask >> Best, >> >> Jim >> >> Donna Toleno wrote: >>> Hello, >>> >>> I am looking for an answer which I believe has been discussed on the list > previously. I would like to know how >> to modify the cdf environment in order to mask out certain probes for a > between species analysis. > > > Thank you for your reply Jim. It has been very helpful. I was able to remove the > unwanted "masked" intensity data by changing the appropriate intensity values to > NA. Then I found that this is not a solution to my problem because RMA will not > accept NA values. So I'm back to modifying the cdf. > > I used the code you pointed me to as well as some related code posted by Ariel > Chernomoretz. When I try things line by line, I have found that there is still a > problem with the following line: > > >> a<-get(pset[i],env=get(cdfpackagename)) > Error in get(x, envir, mode, inherits) : invalid 'envir' argument > > >> cdfpackagename > [1] "mouse4302cdf" >> pset[i] > [1] "1448591_at" > > I wonder what the following lines are for? > > #a<-get(pset[i], env=get(cdfpackagename)) This line gets the pm and mm indices from the cdf package: > a<-get(pset, env=get(cdfpackagename)) > a pm mm [1,] 174302 175304 [2,] 230237 231239 [3,] 530308 531310 [4,] 37779 38781 [5,] 763355 764357 [6,] 230427 231429 [7,] 7137 8139 [8,] 29700 30702 [9,] 987507 988509 [10,] 564747 565749 [11,] 250297 251299 > #a<-a[-iout,] This line removes the rows you don't want for that probeset > #assign(pset[i],a,env=get(cdfpackagename)) This line puts what remains for that probeset back into the cdf environment. > > I thought that I could at least remove the whole probesets without the above > problematic lines. > > so when I try > >> rm(list=listOutProbeSets,envir=get(cdfpackagename)) > > I get a similar error. > > Error in remove(list, envir, inherits) : invalid 'envir' argument > > So I guess my question is what is the valid environment argument? For me, that envir argument works. How about trying just these lines of code on a newly started R session: cdfpackagename <- "mouse4302cdf" pset <- "1448591_at" library(mouse4302cdf) a<-get(pset, env=get(cdfpackagename)) a If that works, then maybe your R session got buggered somehow, and you can then try again. Just to make sure; you are trying to remove probes, not probesets? If you want to remove complete probesets you should look at the altcdfenvs package instead. Best, Jim > >> listOutProbeSets > [1] "1415897_a_at" "1434465_x_at" "1439066_at" > > Could the problem be due to syntax differences. I am using R and Bioconductor on > Windows? > I made a few syntax changes already including a change from "xy2i" to > "xy2indices" based on an error message. Unfortunately, the help files for rm and > for get were not very helpful. > > Any comments would be appreciated. > > Thanks, > > Donna > > _______________________________________________ > 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, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623