Hi, Mark W Kimpel wrote: > I believe I have identified at least one potential contributor to the > problem. In my .Rprofile, the very last like is > "require(affycoretools)". I have this because affycoretools loads so > many of the packages I use every day. When I start R without .Rprofile, > QCReport works fine, but when I use .Rprofile, I get the following slew > of error messages, which I sheepishly have to admit I have been ignoring > because I wasn't having any problems. Of note is the lines: > > "The following object(s) are masked from package:affy : > > barplot," > > It looks to me like some of the base packages are loading after affy and > this is causing problems. Ignoring error/warning messages is really your call, but please do include such information with your initial post - it is kind of important for those of us trying to figure out what has gone wrong. And yes, that does seem to be a part of the problem. You can, and probably should explicitly load the base packages before any others and that should help sort out the masking. > > However, now that I have gotten QCReport to run, I am having trouble > with affyQAReport. I am running R on a Linux machine with 4GB of RAM, > and when I run affyQAReport on 80 rat2302 arrays I get an out of memory > message. When I subset the affybatch down to 16 arrays, I get the > following error Tracking down the memory issue will be harder - basically there are some inefficiencies, but I am not just sure where they might be. If you could run this with options(error=recover) and give some info on where in the computations it is happening that would help - but a quicker fix is going to be more RAM, I think. > > "affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = > "~/Genomics/TL01-05/affyQA", overwrite = FALSE, repName = > "affyQAreport.pdf") > > Error in affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = > "~/Genomics/TL01-05/affyQA", : > could not find function "dist2" This was what I had expected - a bug in genefilter that I finally tracked down on Friday - I think that if you do an update.packages now you will see that you get a new version, and that this error message will go away. > > I agree that this is odd behavior. If you think I should reinstall R and > packages, I'll do it. Below is the full output of my R startup if I have > .Rprofile in play and load affycoretools on bootup. no things should be a bit better now > > Mark > > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Loading required package: utils > [1] "packages do not need updated" > Loading required package: RSPerl > Error in dyn.load(file, ...) : > unable to load shared library > '/home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so': > > /home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so: > undefined symbol: Rf_initEmbeddedR > In addition: There were 18 warnings (use warnings() to see them) > sh: -c: line 0: syntax error near unexpected token `(' > sh: -c: line 0: `./WriteXLS.pl --CSVpath=CSVFILES.tmp/ --CSVfiles=*.csv This is worth reporting to the maintainer of RSPerl > paste(oldwd, TestReport.xls, sep='/')' > Loading required package: affycoretools > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affyio > Loading required package: preprocessCore > Loading required package: limma > Loading required package: GOstats > Loading required package: graph > Loading required package: GO > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: RBGL > Loading required package: Category > Loading required package: KEGG > Loading required package: genefilter > Loading required package: survival > Loading required package: stats > > Attaching package: 'stats' > > > The following object(s) are masked from package:affy : > > update > > Loading required package: graphics > > Attaching package: 'graphics' > > > The following object(s) are masked from package:affy : > > barplot, > boxplot, > hist, > image > > Loading required package: splines > Loading required package: biomaRt > Loading required package: XML > > Attaching package: 'XML' > > > The following object(s) are masked from package:graph : > > addNode > > Loading required package: RCurl > > Attaching package: 'biomaRt' > > > The following object(s) are masked from package:annotate : > > getGO > > Loading required package: gcrma > Loading required package: matchprobes > Loading required package: xtable > Loading required package: annaffy > > Attaching package: 'affycoretools' > > > The following object(s) are masked _by_ .GlobalEnv : > > vennCounts2, > vennSelect > > > if(!exists("baseenv", mode="function")) baseenv <- function() NULL > > options(STERM='iESS', editor='emacsclient') > > > > --- > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> Hi Mark, >> >> Let's see if we cannot fix some of the problems and hopefully life >> will get better. >> >> >> Mark W Kimpel wrote: >>> Seth and Robert, >>> >>> Looks like I may have more than one problem. To clarify one point >>> first, in my original post I was using affy.batch.sub, which >>> consisted of just some of the arrays from my affy.batch. To make sure >>> I'm not having a problem with subsetting, in my subsequent posts I am >>> using the affybatch object created just today with ReadAffy. No old >>> versions here, just what comes out of my sessionInfo(). >>> >>> As you can see below, there may be a problem with my boxplot method >>> but also with the affybatch object. The latter is of class AffyBatch >>> but is not a valid object. >>> >>> Thanks, Mark >>> >>> > class(affy.batch) >>> [1] "AffyBatch" >>> attr(,"package") >>> [1] "affy" >>> >>> > require(affy) >>> > showMethods("boxplot") >>> Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : >>> variable ".AllMTable" was not found >> >> there is something very odd about this - I have not seen it before, >> but it suggests that you might need to do a clean re-install of R and >> packages as something in the methods package (I think) is very confused. >> Not good news, I know, but you should not have this problem. And just >> to be sure this happens if you just start up R, load the affy library >> and then issue the commands above? That is what you need to check. >> >> >> Does this only happen for boxplot? What if you look at >> showMethods(exprs) or something of that nature? >> >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: showMethods("boxplot") >>> 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, >>> inherited, cla >>> 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) >>> >>> >>> > validObject(affy.batch) >>> Error in validObject(affy.batch) : >>> invalid class "AffyBatch" object: sampleNames differ between >>> assayData and phenoData >> >> This is a bit easier to fix. Simply change the sampleNames on one of >> the two structures to be the same as the others. >> >> Basically this is saying that the column names for your expression >> data do not agree with the row names of the phenotypic data. They >> might be different, or they might be out of order. You should look at >> both >> again using the AffyBatch example data: >> >> colnames(exprs(affybatch.example)) >> rownames(pData(affybatch.example)) >> >> need to be the same. If they are not then you need to figure out why >> not and fix them (maybe they are not in the same order, or one of them >> might be missing). >> >> I hope that helps >> >> Robert >> >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: validObject(affy.batch) >>> >>> > par(mfrow=c(2, 1)) >>> > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) >>> > >>> boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>> Index") >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [80] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >>> xlab = "A >>> 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >>> xlab = "A >>> 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = >>> "Log2(Intensity)", x >>> >>> Selection: >>> >>> --- >>> >>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>> Indiana University School of Medicine >>> >>> 15032 Hunter Court, Westfield, IN 46074 >>> >>> (317) 490-5129 Work, & Mobile & VoiceMail >>> (317) 663-0513 Home (no voice mail please) >>> >>> ****************************************************************** >>> >>> Robert Gentleman wrote: >>>> It looks to me like you are using a function named QCReport, not >>>> QAReport (and indeed there is no such thing - you might look at >>>> affyQAReport, which is in the same package but is very different). >>>> >>>> You can try to see what is happening by looking at the code from >>>> signalDist: >>>> >>>> par(mfrow=c(2, 1)) >>>> ArrayIndex = as.character(1:length(sampleNames(object))) >>>> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>>> Index") >>>> >>>> >>>> where instead of object you use affy.batch.sub. The code looks >>>> pretty straightforward, so I don't know what the problem might be. >>>> It is a bit odd, it seems to me to use integers in place of the >>>> sample names... >>>> >>>> I used the affybatch.example and it worked for me.. ( one issue with >>>> that was >>>> Warning message: >>>> In data.row.names(row.names, rowsi, i) : >>>> some row.names duplicated: >>>> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,42 6,451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >>>> >>>> .... >>>> >>>> which we may need to look at). >>>> >>>> best wishes >>>> Robert >>>> >>>> >>>> Mark W Kimpel wrote: >>>>> I am running into an error when I run QAReport on an affybatch >>>>> object. Below is my sessionInfo and output. I am using the devel >>>>> versions of R and BioC, all newly updated. Please advise. >>>>> >>>>> Thanks, >>>>> Mark >>>>> >>>>> Browse[1]> sessionInfo() >>>>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>>>> i686-pc-linux-gnu >>>>> >>>>> locale: >>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE =en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER= en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US .UTF-8;LC_IDENTIFICATION=C >>>>> >>>>> >>>>> attached base packages: >>>>> [1] grDevices datasets splines graphics stats tools utils >>>>> [8] methods base >>>>> >>>>> other attached packages: >>>>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 >>>>> affyQCReport_1.15.2 >>>>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>>>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>>>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>>>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>>>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>>>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>>>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>>>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>>>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>>>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>>>> [34] Biobase_1.15.21 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>>>> >>>>> > affy.batch.sub >>>>> AffyBatch object >>>>> size of arrays=834x834 features (14 kb) >>>>> cdf=Rat230_2 (31099 affyids) >>>>> number of samples=16 >>>>> number of genes=31099 >>>>> annotation=rat2302 >>>>> notes= >>>>> > QCReport(affy.batch.sub) >>>>> Error in attr(groups, "names") <- names : >>>>> 'names' attribute [16] must be the same length as the vector [1] >>>>> >>>>> Enter a frame number, or 0 to exit >>>>> >>>>> 1: QCReport(affy.batch.sub) >>>>> 2: signalDist(object) >>>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", >>>>> xlab = "Array >>>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>>> "Log2(Intensity)", xlab >>>>> >>>>> Selection: 4 >>>>> Called from: eval(expr, envir, enclos) >>>>> Browse[1]> ls() >>>>> [1] "add" "args" "at" "border" "col" >>>>> [6] "groups" "horizontal" "log" "n" "namedargs" >>>>> [11] "names" "notch" "outline" "pars" "plot" >>>>> [16] "range" "*tmp*" "varwidth" "width" "x" >>>>> Browse[1]> names >>>>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>>>> "13" "14" "15" >>>>> [16] "16" >>>>> Browse[1]> names(group) >>>>> NULL >>>>> Browse[1]> names(groups) >>>>> [1] "" >>>>> Browse[1]> names(groups) <- names >>>>> Error during wrapup: 'names' attribute [16] must be the same length >>>>> as the vector [1] >>>>> Browse[1]> >>>> >>> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org