Harry Mangalam <harry.mangalam at="" ...=""> writes: > > Hi Jim, > > Thanks for the rapid reply, info and pointers. > > I tried to take your advice and on a larger machine (due to malloc > errors on the 1st - new sessionInfo() below) I can get a bit further > but still can't convince arrayQualityMetrics() to take or recognize > the appropriate cdf env. > > While I include the entire session below, the main problem seems to be > that R will not conclude the installation of the CDF you referenced: > > biocLite("mogene10stv1cdf") > > either referenced separately or as part of the arrayQualityMetrics() > dependency. It gave the identical results on the machine I used > before (w/ R 2.11.1) and on the larger 64b machine (w/ R 2.11.0). > > The entire session follows. > (From a clean start on the machine whose sessionInfo() is included at > beginning and end of the session.) > > $ module load R/2.11.0 # we use modules to keep things separate > $ R > > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] graphics grDevices datasets stats utils methods base > > other attached packages: > [1] Rmpi_0.5-8 > > >library(affy) > ># deleted all 'std' output, including only errors or warnings. > > #create an affybatch object from the cel files. > > ab <- ReadAffy(widget=TRUE) # select all 8 wt cels (sal vs coc) > > > library("arrayQualityMetrics") > # and run the code on all the wt cels > > arrayQualityMetrics(expressionset = ab,outdir = "wt_sal_v_coc",force > = TRUE,do.logtransform = TRUE) > Loading required package: affyPLM > Loading required package: gcrma > Loading required package: preprocessCore > > Attaching package: 'affyPLM' > > The following object(s) are masked from 'package:stats': > > resid, residuals, weights > > >arrayQualityMetrics(expressionset = ab,outdir = "wt_sal_v_coc",force > = TRUE,do.logtransform = TRUE) > The report will be written in directory 'wt_sal_v_coc'. > trying URL > 'http://bioconductor.org/packages/2.6/data/annotation/src/contrib/moge ne10stv1cdf_2.6.2.tar.gz' > Content type 'application/x-gzip' length 3126174 bytes (3.0 Mb) > opened URL > ================================================== > downloaded 3.0 Mb > > * installing *source* package ?mogene10stv1cdf? ... > ** R > ** data > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : > object 'annoStartupMessages' not found > ERROR: loading failed > * removing ?/apps/R/2.11.0/lib64/R/library/mogene10stv1cdf? > > The downloaded packages are in > ?/tmp/Rtmpq2sQrq/downloaded_packages? > Updating HTML index of packages in '.Library' > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MoGene-1_0-st-v1 > Library - package mogene10stv1cdf not installed > Library - package mogene10stv1cdf not installed > In addition: Warning message: > In install.packages(cdfname, lib = lib, repos = > Biobase:::biocReposList(), : > installation of package 'mogene10stv1cdf' had non-zero exit status > > <<the above="" stanza="" repeated="" 2="" more="" times,="" downloading="" and="" then="" failing=""> to install the same pkg>> > > Is this a problem with matching case and intervening characters? > (mogene10stv1 vs MoGene-1_0-st-v1) or something more fundamental. > > I tried this as a user and as root, to see if it was a permissions > problem. The results were identical. > > I also tried the installation of the CDF that came with the cel files. > (MoGene-1_0-st-v1.r3.cdf), but while this apparently went to > completion (as previously noted), it did not change anything. > > # at end of session, here is the sessionInfo() Hi Jim, Harry, I have the same problem. I am using the drosogenome2cdf file and try to work with the drosophila genome 2.0 genechip arrays. I tried to run QCreport (package - affyQCReport) on my data and got the message: Error in setQCEnvironment(cdfn) : Could not find array definition file ' drosophila2cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. I than did as said in the manual and used setQCEnvironment (package - simpleaffy) to set it to the drosogenome2cdf environment). setQCEnvironment("drosgenome2cdf", getwd()) # it was saved in my wd. I tried again and got the same error message as Harry: Error: NAs in foreign function call (arg 5) Why can't I use this environment to analyze my data? Is there a better package to pre-check my CEl files for their quality? THX in advance > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] drosophila2cdf_2.7.0 affyQCReport_1.28.0 lattice_0.19-13 [4] simpleaffy_2.26.0 gcrma_2.22.0 genefilter_1.32.0 [7] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 affyPLM_1.26.0 annotate_1.28.0 [4] AnnotationDbi_1.12.0 Biostrings_2.18.0 DBI_0.2-5 [7] grid_2.12.0 IRanges_1.8.2 preprocessCore_1.10.0 [10] RColorBrewer_1.0-2 RSQLite_0.9-1 splines_2.12.0 [13] survival_2.35-8 tools_2.12.0 xtable_1.5-6 Assa