James W. MacDonald wrote: > Hi Sanchita, > > Sanchita Bhattacharya wrote: > >>Hi, >> >> >>I have a question about running the QCReport funtion in R 2.5. I work with >>HTHgu133 arrays ( High throughput arrays) and I was trying to get the >>QCReport for those arrays. I uploaded HTHgu133Av2 cdf to run this function. >>But still I am getting error which is pasted below: >> >> >> >>>QCReport(Data,file="testReport.pdf") >> >>Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip >>type: hthgu133acdf >>Error in plot(qc(object)) : error in evaluating the argument 'x' in >>selecting a method for function 'plot > > > This means that simpleaffy doesn't know about these chips. A hackish way > around this (not tested, so if it doesn't work, don't blame me ;-D) is > to over-write the .qcEnv that contains these qc parameters. > > > library(simpleaffy) > > df1 <- get("alpha", .qcEnv) > > df2 <- get("qc.probes", .qcEnv) > > qc3 <- get("spikes", .qcEnv) > > df1 <- rbind(df1, "hthgu133acdf" = df1[6,]) > > df2 <- rbind(df2, "hthgu133acdf" = df2[6,]) > > df3 <- rbind(df3, "hthgu133acdf" = df3[6,]) > > .qcEnv <- new.env(hash=TRUE) > > multiassign(c("alpha","qc.probes","spikes"), c(df1, df2, df3), .qcEnv) > > Here we are just using the hgu133a chip data which I think should be the > same (my understanding is the HT chip is just a bunch of the 'regular' > chips cobbed together). If this works, you could write a little function > to do it automatically. I should probably elaborate a bit here. The .qcEnv is a little environment containing three data.frames that hold certain data that simpleaffy uses. What I show here is hackish because you will just be over-writing this env with one containing the data you need, and this will not persist beyond the current R session. Slightly less hackish would be to get the sources for simpleaffy, create the env as above, save it, replace the one that comes with simpleaffy and re-install. This is slightly more work, and even more if you are on Windows and not set up to build packages. However, the changes you made would be persistent over different R sessions until you upgrade simpleaffy. Even less hackish would be to make the env as described above and then contribute it to Crispin Miller, the maintainer of simpleaffy. This way your changes would persist in perpetuity and others would benefit as well. Best, Jim > > Best, > > Jim > > > >> >>I will appreciate if somebody can help me to debug this problem. >> >> >>Thanks, >> >>Sanchita >> >>_______________________________________________ >>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 University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.