It looks like your cdf files don't match your gene type. Specifically, your mouse cdfs look like they are for the Exon array but you've set up all your folder directories for the Gene array. Probably if you get the correct cdfs it will will work fine. Elizabeth
chunjiang he wrote: > Thanks so much for the patient answers. > > I think there are some problems with my environment path. I have put all > my data and CDF in directories strictly as yours. But the problem is > also the same. I checked my CDF files. > I put 5 files in the /annotationData/chipTypes/MoGene-1_0-st-v1: > > MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf > MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf > MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf > MoEx-1_0-st-v1,U-Ensembl50,G-Affy,EP.cdf > MoEx-1_0-st-v1.cdf > > I think the *,monocell.cdf may be created automatically when I run the > scripts. > > And i put all the CEL files in /rawData/JunXu/MoGene-1_0-st-v1. So I > think it is no problem. But does the script can recognize the path > automatically, or I must indicate it in R scripts? > On Thu, May 14, 2009 at 2:38 PM, Lakshmanan Iyer <lax...@gmail.com > <mailto:lax...@gmail.com>> wrote: > > Hi > Put the raw data, CEL files in, > C:/Documents and Settings/rawData/JunXu/MoGene-1_0-st-v1 > > and annotatino file, CDF files, in > C:/Documents and Settings/annotationData/chipTypes/MoGene-1_0-st-v1 > > Copy the R-script below in note book and save it as "myscript.R" > > Now Launch R > Change Working directory to C:/Documents and Settings > use the R command: > source ("myscript.R") > to execute the commands and it should work. > > I am afraid, I am making this up from my previous experience working > with PCs. > > -Best > -Lax > > > On Thu, May 14, 2009 at 3:00 PM, chunjiang he <camel...@gmail.com > <mailto:camel...@gmail.com>> wrote: > > Thanks very much, > But how could I set my data path and array path in windows. I > mean how to set it when I use R. > when I run this: > > > cdf<-AffymetrixCdfFile$fromChipType(chipType) > > I got the error: > > Error in list(`AffymetrixCdfFile$fromChipType(chipType)` = > <environment>, : > > [2009-05-14 13:57:50] Exception: Could not locate a file for > this chip type: MoGene-1_0-st-v1 > at throw(Exception(...)) > at throw.default("Could not locate a file for this chip type: > ", paste(c(chipT > at throw("Could not locate a file for this chip type: ", > paste(c(chipType, tag > at byChipType.UnitNamesFile(static, ...) > at byChipType(static, ...) > at method(static, ...) > at AffymetrixCdfFile$fromChipType(chipType) > > Best, > Jiang > > On Thu, May 14, 2009 at 12:45 PM, Lakshmanan Iyer > <lax...@gmail.com <mailto:lax...@gmail.com>> wrote: > > Hi, > Hope this helps! > Here is how I ran a Affy, MoGene-1_0-st chip analysis on a > ubuntu/linux box: > Please double check the code to make sure that it is fine! I > have not looked at it for a long time. > -Best > -Lax > ________________________________________________________________ > The CEL file (JC1.CEL JC2.CEL NC1.CEL NC2.CEL) are in: > /home/laxman/Projects/Analysis/rawData/JunXu/MoGene-1_0-st-v1 > > The annotation files, CDF files, (MoGene-1_0-st-v1.cdf > MoGene-1_0-st-v1,monocell.CDF) are in: > > /home/laxman/Projects/Analysis/annotationData/chipTypes/MoGene-1_0-st-v1 > > Directory in which I am running the jobs. Contains the R > script file, see below: > /home/laxman/Projects/Analysis > Pay attention to the line following: #<<<<<<<<<<<<<<<<< > > The results would be found in: > /home/laxman/Projects/Analysis/Results/JunXu > > > ##################################################################### > # Script to calculate probeset level/gene level intensities > #Based on > > http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis > #Load the library > library(aroma.affymetrix) > verbose <- Arguments$getVerbose(-8) > timestampOn(verbose) > # > #<<<<<<<<<<<<<<<<< > #setup the CDF explicitly as: > chipType <- "MoGene-1_0-st-v1" > cdf <- AffymetrixCdfFile$fromChipType(chipType) > # > #Next we setup the CEL set with the above custom CDF: > ##<<<<<<<<<<<< > cs <- AffymetrixCelSet$fromName("JunXu", cdf=cdf) > setCdf(cs,cdf) > # > #In order to do RMA background correction, we setup a > correction method and runs it by: > # > bc <- RmaBackgroundCorrection(cs) > csBC <- process(bc,verbose=verbose) > #Note that this is the first step where we will create new > files, > #so we have put in a tag that should follow through the rest > of the analysis. > # > #We then setup a quantile normalization method: > qn <- QuantileNormalization(csBC, typesToUpdate="pm") > print(qn) > # > #and we then run it by: > csN <- process(qn, verbose=verbose) > print (csN) > # > #You can check associated CSF with the command > getCdf(csN) > # > #To fit a summary of the entire transcript (i.e. estimate > the overall expression for the transcript), do > plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) > print(plmTr) > # > #Otherwise, to fit exon-by-exon, change the value of > mergeGroups to FALSE in the ExonRmaPlm() call above. > # > # plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE) > # print(plmEx) > # > #To fit the PLM to all of the data, do: > # > fit(plmTr, verbose=verbose) > # > #or similarly for plmEx. > # fit(plmEx, verbose=verbose) > # > #Quality assessment of PLM fit > # > #To calculate the residuals from the PLM fit, do: > # > rs <- calculateResiduals(plmTr, verbose=verbose) > # > #To browse spatial false-colored images of the residuals, do: > ae <- ArrayExplorer(rs) > setColorMaps(ae, c("log2,log2neg,rainbow", > "log2,log2pos,rainbow")) > process(ae, interleaved="auto", verbose=verbose) > # display(ae) > # > #To examine NUSE and RLE plots, do > #Note that this can be done to fits based on the transcript > level > #or exon level depending on which plm you chose and can give > different interpretations. > qamTr <- QualityAssessmentModel(plmTr) > # save plots in pdf file > > pdf(file="/home/laxman/Projects/Analysis/Results/JunXu/NusePlot.pdf"); > plotNuse(qamTr) > > pdf(file="/home/laxman/Projects/Analysis/Results/JunXu/RlePlot.pdf"); > plotRle(qamTr) > dev.off() > # turned pdf off > # > # > #To extract the estimates (transcript or probeset) > #use either extractMatrix() or extractDataFrame() on the > ChipEffectSet that corresponds to the plm object: > #This will give a data.frame with three rows, each row > corresponding to a unit/transcript > # > cesTr <- getChipEffectSet(plmTr) > trFit <- extractDataFrame(cesTr, addNames=TRUE) > write.table > > (trFit[,c(1,6:9)],"/home/laxman/Projects/Analysis/Results/JunXu/trFit.tsv", > sep="\t", quote=F) > > # > #To get estimates of the probesets/exons > #you must choose mergeGroups=FALSE as described > #above when you define your plm object, and then extract the > estimates from it. > # > # cesEx <- getChipEffectSet(plmEx) > # exFit <- > extractDataFrame(cesEx,units=1:3,addNames=TRUE) > # > #Alternative Splicing Analysis (FIRMA) > firma <- FirmaModel(plmTr) > fit(firma, verbose=verbose) > fs <- getFirmaScores(firma) > x <- extractDataFrame(fs) > > On Thu, May 14, 2009 at 12:25 PM, chunjiang he > <camel...@gmail.com <mailto:camel...@gmail.com>> wrote: > > Hi all, > I am sorry I cannot understand the path of data > directory of aroma.affymetrix. Such as > > annotationData/chipTypes/<chip type>/ > > what does this sentence mean? where I can put mouse CDF > files? I am using windows vista. > > And what is the following mean: > > > <data set path> = <path>/<data set name>(,tag)*/ > <array set path> = <data set path>/<chip type>/ > > where I can set them? > > Thanks very much. > > jiang > > > > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
