That is a good point Martin. Jim what version of AnnotationDbi do you have installed for R-2-11 beta? Marc On 09/22/2010 11:34 AM, Martin Morgan wrote: > On 09/22/2010 10:55 AM, James W. MacDonald wrote: > >> Hi Marc, >> >> On 9/22/2010 1:23 PM, Marc Carlson wrote: >> >>> Hi guys, >>> >>> Strangely enough I do not get this error from here in Seattle (on >>> openSUSE). >>> >> Yeah, well that's because your skillz are vastly superior to mine ;-D >> >> So if I wget the tarball from below and use install.packages, I get >> >> >>> install.packages("mogene10stv1cdf_2.6.2.tar.gz", repos=NULL) >>> >> Warning in install.packages("mogene10stv1cdf_2.6.2.tar.gz", repos = NULL) : >> argument 'lib' is missing: using '/home/jwm/R-2.11.0libs' >> * 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 >> > I think annoStartupMessages was added in AnnotationDbi 1.10.1, so > perhaps this is just a version mismatch? > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > Martin > > >> ERROR: loading failed >> * removing '/home/jwm/R-2.11.0libs/mogene10stv1cdf' >> * restoring previous '/home/jwm/R-2.11.0libs/mogene10stv1cdf' >> Warning message: >> In install.packages("mogene10stv1cdf_2.6.2.tar.gz", repos = NULL) : >> installation of package 'mogene10stv1cdf_2.6.2.tar.gz' had non- zero >> exit status >> >> >> However, if I point to the package I made here: >> >> >>> >> install.packages("~/BioC/archived_cdfs/build/mogene10stv1cdf_2.6.0. tar.gz", >> repos=NULL) >> Warning in >> install.packages("~/BioC/archived_cdfs/build/mogene10stv1cdf_2.6.0. tar.gz", >> : >> argument 'lib' is missing: using '/home/jwm/R-2.11.0libs' >> * 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 >> >> * DONE (mogene10stv1cdf) >> >> >>> sessionInfo() >>> >> R version 2.11.0 beta (2010-04-11 r51685) >> i686-pc-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tools_2.11.0 >> >> Best, >> >> Jim >> >> >> >>> The tarballs for all the annotation packages can always be found on our >>> web site if biocLite should ever fail you (or if you just want to see >>> what is in the source code): >>> >>> http://www.bioconductor.org/packages/release/data/annotation/ >>> >>> >>> I also see that Harry is not using the most recent version of >>> AnnotationDbi for your version of R, so you might want to try and update >>> that as well. >>> >>> biocLite("AnnotationDbi") >>> >>> >>> Also, since I can't reproduce the behavior that you guys are >>> experiencing, could you please let us know whatever you can about it? >>> >>> >>> Marc >>> >>> >>> >>> On 09/21/2010 02:08 PM, James W. MacDonald wrote: >>> >>>> Hi Harry, >>>> >>>> I get the same error you see, when I try to install on Linux. Weirdly >>>> enough, if I install from source on my Windows box I don't have any >>>> problems. >>>> >>>> And even weirder, I can install the source package on Linux if I use >>>> my local copy (I make the cdf packages for BioC, so I have the >>>> packages that I uploaded in April still sitting around). >>>> >>>> I would assume some corruption, if the package didn't install on >>>> Windows, but it does. >>>> >>>> Well, anyway, attached is the package that will install for me. See if >>>> it works for you. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>> On 9/21/2010 3:55 PM, Harry Mangalam wrote: >>>> >>>>> 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/contri b/mogene10stv1cdf_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() >>>>> >>>>>> 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] tools tcltk graphics grDevices datasets stats utils >>>>> [8] methods base >>>>> >>>>> other attached packages: >>>>> [1] arrayQualityMetrics_2.6.0 affyPLM_1.24.1 >>>>> [3] preprocessCore_1.10.0 gcrma_2.20.0 >>>>> [5] tkWidgets_1.26.0 DynDoc_1.26.0 >>>>> [7] widgetTools_1.26.0 affy_1.26.1 >>>>> [9] Biobase_2.8.0 Rmpi_0.5-8 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.0 >>>>> [4] beadarray_1.16.0 Biostrings_2.16.9 DBI_0.2-5 >>>>> [7] genefilter_1.30.0 grid_2.11.0 hwriter_1.2 >>>>> [10] IRanges_1.6.17 lattice_0.18-5 latticeExtra_0.6-11 >>>>> [13] limma_3.4.5 marray_1.26.0 RColorBrewer_1.0-2 >>>>> [16] RSQLite_0.8-4 simpleaffy_2.24.0 splines_2.11.0 >>>>> [19] stats4_2.11.0 survival_2.35-8 vsn_3.16.0 >>>>> [22] xtable_1.5-6 >>>>> >>>>> Thanks for your consideration. >>>>> >>>>> harry >>>>> >>>>> >>>>> On Tuesday 21 September 2010 06:49:38 James W. MacDonald wrote: >>>>> >>>>>> Hi Harry, >>>>>> >>>>>> On 9/20/2010 6:20 PM, Harry Mangalam wrote: >>>>>> >>>>>>> Hi BioC >>>>>>> >>>>>>> (sessionInfo() at bottom) >>>>>>> >>>>>>> I'm trying to help a group here do some QC on their affy datasets >>>>>>> derived from the mogene10stv1 array set. This array is not in >>>>>>> mainstream BioC support but I've created and installed the CDF >>>>>>> >>>>>> >>>>>>> environment for that array: >>>>>>> >>>>>> This is not correct. >>>>>> >>>>>> biocLite("mogene10stv1cdf") >>>>>> >>>>>> Will get you the package you create below. >>>>>> >>>>>> >>>>>>>> make.cdf.package("MoGene-1_0-st-v1.r3.cdf", species = >>>>>>>> "Mus_mus") >>>>>>>> >>>>>>> (completes, and I've installed the generated CDF env) >>>>>>> >>>>>>> but when I try to run QCReport on this dataset (even explicitly >>>>>>> >>>>>> >>>>>>> specifying the mogene10stv1 CDF env), I get the errors: >>>>>>> >>>>>> In future, please mention the package you are using. I happen to >>>>>> know that QCReport() is part of the affyQCReport package, but by >>>>>> neglecting to include this bit of information you seriously >>>>>> degrade your chances of an answer. >>>>>> >>>>>> Now on to the answer. ;-D >>>>>> >>>>>> You are not going to be very satisfied with affyQCReport for this >>>>>> chip, as it uses the simpleaffy package for much of the quality >>>>>> control output, a good portion of which is based on MAS5 calls. >>>>>> Since the MoGene chip is a PM-only chip, you won't be able to >>>>>> compute MAS5 calls, as they rely on the matching MM probes, which >>>>>> don't exist. Hence the NA values below. >>>>>> >>>>>> I believe you will be better off using the arrayQualityMetrics >>>>>> package, which is more general. >>>>>> >>>>>> Best, >>>>>> >>>>>> Jim >>>>>> >>>>>> >>>>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf")) >>>>>>>> >>>>>>> # or >>>>>>> >>>>>>> >>>>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1")) >>>>>>>> >>>>>>> # (get same error) >>>>>>> >>>>>>> Error: NAs in foreign function call (arg 1) >>>>>>> In addition: Warning messages: >>>>>>> >>>>>>> 1: In data.row.names(row.names, rowsi, i) : >>>>>>> some row.names duplicated: >>>>>>> 4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50 >>>>>>> ,51,52,53,54,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,9 >>>>>>> 4,95,96,97,98,99,102,103,104,108,109,110,111,114,119,120,121,122, >>>>>>> 127,134,136,137,138,139,141,142,147,148,149,152,153,156,157,158,1 >>>>>>> 59,162,163,164,165,166,167,168,169,170,171,173,175,176,179,180,18 >>>>>>> 3,184,185,186,191,192,195,197,198,199,200,202,206,207,210,219,220 >>>>>>> ,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,251, >>>>>>> 252,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,2 >>>>>>> 90,291,292,296,297,298,302,304,305,306,310,311,312,313,317,318,31 >>>>>>> 9,321,322,324,334,337,338,339,340,341,345,346,350,351,356,359,362 >>>>>>> ,364,366,367,370,371,373,376,378,382,383,384,385,386,387,388,389, >>>>>>> 391,394,395,397,398,399,400,402,403,405,406,407,409,410,411,415,4 >>>>>>> 16,418,419,425,431,432,433,434,435,440,441,443,445,447,449,450,45 >>>>>>> 2,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,494 >>>>>>> ,495,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51 >>>>>>> [... truncated] >>>>>>> >>>>>>> 2: In qc.affy(unnormalised, ...) : >>>>>>> CDF Environment name ' hgu95av2cdf ' does not match cdfname ' >>>>>>> >>>>>>> mogene10stv1cdf ' >>>>>>> >>>>>>> Error in plot(qc(object)) : >>>>>>> error in evaluating the argument 'x' in selecting a method for >>>>>>> >>>>>>> function 'plot' >>>>>>> >>>>>>> >>>>>>> This: /Error: NAs in foreign function call (arg 1)/ >>>>>>> >>>>>>> seems to imply that: >>>>>>> - there's an error in the '(arg 1)' but which (arg 1)? >>>>>>> >>>>>>> If this refers to the arg >>>>>>> >>>>>>> /ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf")/ >>>>>>> >>>>>>> then that part of the command seems to complete fine and >>>>>>> returns an >>>>>>> >>>>>>> AffyBatch object as it should >>>>>>> >>>>>>> >>>>>>>> str(rawdata) >>>>>>>> >>>>>>> Formal class 'AffyBatch' [package "affy"] with 10 slots >>>>>>> >>>>>>> ..@ cdfName : chr "mogene10stv1cdf" >>>>>>> ..@ nrow : int 1050 >>>>>>> ..@ ncol : int 1050 >>>>>>> >>>>>>> /etc/ >>>>>>> >>>>>>> >>>>>>> - or I have NAs in the data, but doesn't point to where or >>>>>>> whether I should address them. >>>>>>> If this is the critical error, I'm guessing I have to choose a >>>>>>> transform that removes or floor-shifts the NAs into a >>>>>>> computational form? >>>>>>> >>>>>>> - the Warnings: >>>>>>> >>>>>>> 1: In data.row.names(row.names, rowsi, i) : >>>>>>> some row.names duplicated: >>>>>>> 4,8,9,13,14,15,16,24,25,26,27,28,29,<almost every="">>>>>>> intervening # omitted> >>>>>>> ,513,515,516,51 [... truncated] >>>>>>> >>>>>>> Would this be related to warning 2 below? >>>>>>> >>>>>>> 2: In qc.affy(unnormalised, ...) : >>>>>>> CDF Environment name ' hgu95av2cdf ' does not match cdfname ' >>>>>>> >>>>>>> mogene10stv1cdf ' >>>>>>> >>>>>>> but if so, what is the proper way to tell QCReport that I'm using >>>>>>> a non-default CDF? >>>>>>> the help section for QCReport doesn't describe any params for >>>>>>> telling it that the CDF env is not 'hgu95av2cdf' and I've tried >>>>>>> including that info in the ReadAffy() fn as noted: >>>>>>> >>>>>>> ie: >>>>>>> >>>>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1")) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> sessionInfo() >>>>>>>> >>>>>>> R version 2.11.1 (2010-05-31) >>>>>>> i486-pc-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] tools tcltk stats graphics grDevices utils >>>>>>> datasets >>>>>>> [8] methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] makecdfenv_1.26.0 tkWidgets_1.26.0 DynDoc_1.26.0 >>>>>>> [4] widgetTools_1.26.0 hgu95av2cdf_2.6.0 >>>>>>> affydata_1.11.10 [7] affyQCReport_1.26.0 lattice_0.19-11 >>>>>>> RColorBrewer_1.0-2 >>>>>>> >>>>>>> [10] affyPLM_1.24.1 preprocessCore_1.10.0 xtable_1.5-6 >>>>>>> [13] simpleaffy_2.24.0 gcrma_2.20.0 >>>>>>> genefilter_1.30.0 [16] mogene10stv1cdf_2.6.2 affy_1.26.1 >>>>>>> Biobase_2.8.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.16.0 annotate_1.26.1 >>>>>>> AnnotationDbi_1.10.2 [4] Biostrings_2.16.9 DBI_0.2-5 >>>>>>> grid_2.11.1 [7] IRanges_1.6.17 RSQLite_0.9-2 >>>>>>> splines_2.11.1 >>>>>>> >>>>>>> [10] survival_2.35-8 >>>>>>> >>>>>>> >>>>>>> Thanks for your consideration. >>>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >>> >> >

Hi Martin, On 9/22/2010 2:34 PM, Martin Morgan wrote: > On 09/22/2010 10:55 AM, James W. MacDonald wrote: >> Hi Marc, >> >> On 9/22/2010 1:23 PM, Marc Carlson wrote: >>> Hi guys, >>> >>> Strangely enough I do not get this error from here in Seattle (on >>> openSUSE). >> >> Yeah, well that's because your skillz are vastly superior to mine ;-D >> >> So if I wget the tarball from below and use install.packages, I get >> >>> install.packages("mogene10stv1cdf_2.6.2.tar.gz", repos=NULL) >> Warning in install.packages("mogene10stv1cdf_2.6.2.tar.gz", repos = NULL) : >> argument 'lib' is missing: using '/home/jwm/R-2.11.0libs' >> * 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 > > I think annoStartupMessages was added in AnnotationDbi 1.10.1, so > perhaps this is just a version mismatch? And right you are! <curmudgeon> Grrr. Adding functionality mid-release grumble grumble. Unfortunately we are a couple of days past 'Talk like a Pirate day' or I would have to add Arrgh, Matey, keelhaul the scurvy dogs! as well ;-D </curmudgeon> Harry - just follow the instructions at the below URL, and you will be able to install the mogene cdf package using biocLite(), as usual. Best, Jim > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > Martin > >> ERROR: loading failed >> * removing '/home/jwm/R-2.11.0libs/mogene10stv1cdf' >> * restoring previous '/home/jwm/R-2.11.0libs/mogene10stv1cdf' >> Warning message: >> In install.packages("mogene10stv1cdf_2.6.2.tar.gz", repos = NULL) : >> installation of package 'mogene10stv1cdf_2.6.2.tar.gz' had non- zero >> exit status >> >> >> However, if I point to the package I made here: >> >>> >> install.packages("~/BioC/archived_cdfs/build/mogene10stv1cdf_2.6.0. tar.gz", >> repos=NULL) >> Warning in >> install.packages("~/BioC/archived_cdfs/build/mogene10stv1cdf_2.6.0. tar.gz", >> : >> argument 'lib' is missing: using '/home/jwm/R-2.11.0libs' >> * 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 >> >> * DONE (mogene10stv1cdf) >> >>> sessionInfo() >> R version 2.11.0 beta (2010-04-11 r51685) >> i686-pc-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tools_2.11.0 >> >> Best, >> >> Jim >> >> >>> >>> The tarballs for all the annotation packages can always be found on our >>> web site if biocLite should ever fail you (or if you just want to see >>> what is in the source code): >>> >>> http://www.bioconductor.org/packages/release/data/annotation/ >>> >>> >>> I also see that Harry is not using the most recent version of >>> AnnotationDbi for your version of R, so you might want to try and update >>> that as well. >>> >>> biocLite("AnnotationDbi") >>> >>> >>> Also, since I can't reproduce the behavior that you guys are >>> experiencing, could you please let us know whatever you can about it? >>> >>> >>> Marc >>> >>> >>> >>> On 09/21/2010 02:08 PM, James W. MacDonald wrote: >>>> Hi Harry, >>>> >>>> I get the same error you see, when I try to install on Linux. Weirdly >>>> enough, if I install from source on my Windows box I don't have any >>>> problems. >>>> >>>> And even weirder, I can install the source package on Linux if I use >>>> my local copy (I make the cdf packages for BioC, so I have the >>>> packages that I uploaded in April still sitting around). >>>> >>>> I would assume some corruption, if the package didn't install on >>>> Windows, but it does. >>>> >>>> Well, anyway, attached is the package that will install for me. See if >>>> it works for you. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>> On 9/21/2010 3:55 PM, Harry Mangalam wrote: >>>>> 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/contri b/mogene10stv1cdf_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() >>>>>> 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] tools tcltk graphics grDevices datasets stats utils >>>>> [8] methods base >>>>> >>>>> other attached packages: >>>>> [1] arrayQualityMetrics_2.6.0 affyPLM_1.24.1 >>>>> [3] preprocessCore_1.10.0 gcrma_2.20.0 >>>>> [5] tkWidgets_1.26.0 DynDoc_1.26.0 >>>>> [7] widgetTools_1.26.0 affy_1.26.1 >>>>> [9] Biobase_2.8.0 Rmpi_0.5-8 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.0 >>>>> [4] beadarray_1.16.0 Biostrings_2.16.9 DBI_0.2-5 >>>>> [7] genefilter_1.30.0 grid_2.11.0 hwriter_1.2 >>>>> [10] IRanges_1.6.17 lattice_0.18-5 latticeExtra_0.6-11 >>>>> [13] limma_3.4.5 marray_1.26.0 RColorBrewer_1.0-2 >>>>> [16] RSQLite_0.8-4 simpleaffy_2.24.0 splines_2.11.0 >>>>> [19] stats4_2.11.0 survival_2.35-8 vsn_3.16.0 >>>>> [22] xtable_1.5-6 >>>>> >>>>> Thanks for your consideration. >>>>> >>>>> harry >>>>> >>>>> >>>>> On Tuesday 21 September 2010 06:49:38 James W. MacDonald wrote: >>>>>> Hi Harry, >>>>>> >>>>>> On 9/20/2010 6:20 PM, Harry Mangalam wrote: >>>>>>> Hi BioC >>>>>>> >>>>>>> (sessionInfo() at bottom) >>>>>>> >>>>>>> I'm trying to help a group here do some QC on their affy datasets >>>>>>> derived from the mogene10stv1 array set. This array is not in >>>>>>> mainstream BioC support but I've created and installed the CDF >>>>>> >>>>>>> environment for that array: >>>>>> This is not correct. >>>>>> >>>>>> biocLite("mogene10stv1cdf") >>>>>> >>>>>> Will get you the package you create below. >>>>>> >>>>>>>> make.cdf.package("MoGene-1_0-st-v1.r3.cdf", species = >>>>>>>> "Mus_mus") >>>>>>> >>>>>>> (completes, and I've installed the generated CDF env) >>>>>>> >>>>>>> but when I try to run QCReport on this dataset (even explicitly >>>>>> >>>>>>> specifying the mogene10stv1 CDF env), I get the errors: >>>>>> In future, please mention the package you are using. I happen to >>>>>> know that QCReport() is part of the affyQCReport package, but by >>>>>> neglecting to include this bit of information you seriously >>>>>> degrade your chances of an answer. >>>>>> >>>>>> Now on to the answer. ;-D >>>>>> >>>>>> You are not going to be very satisfied with affyQCReport for this >>>>>> chip, as it uses the simpleaffy package for much of the quality >>>>>> control output, a good portion of which is based on MAS5 calls. >>>>>> Since the MoGene chip is a PM-only chip, you won't be able to >>>>>> compute MAS5 calls, as they rely on the matching MM probes, which >>>>>> don't exist. Hence the NA values below. >>>>>> >>>>>> I believe you will be better off using the arrayQualityMetrics >>>>>> package, which is more general. >>>>>> >>>>>> Best, >>>>>> >>>>>> Jim >>>>>> >>>>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf")) >>>>>>> >>>>>>> # or >>>>>>> >>>>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1")) >>>>>>> >>>>>>> # (get same error) >>>>>>> >>>>>>> Error: NAs in foreign function call (arg 1) >>>>>>> In addition: Warning messages: >>>>>>> >>>>>>> 1: In data.row.names(row.names, rowsi, i) : >>>>>>> some row.names duplicated: >>>>>>> 4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50 >>>>>>> ,51,52,53,54,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,9 >>>>>>> 4,95,96,97,98,99,102,103,104,108,109,110,111,114,119,120,121,122, >>>>>>> 127,134,136,137,138,139,141,142,147,148,149,152,153,156,157,158,1 >>>>>>> 59,162,163,164,165,166,167,168,169,170,171,173,175,176,179,180,18 >>>>>>> 3,184,185,186,191,192,195,197,198,199,200,202,206,207,210,219,220 >>>>>>> ,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,251, >>>>>>> 252,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,2 >>>>>>> 90,291,292,296,297,298,302,304,305,306,310,311,312,313,317,318,31 >>>>>>> 9,321,322,324,334,337,338,339,340,341,345,346,350,351,356,359,362 >>>>>>> ,364,366,367,370,371,373,376,378,382,383,384,385,386,387,388,389, >>>>>>> 391,394,395,397,398,399,400,402,403,405,406,407,409,410,411,415,4 >>>>>>> 16,418,419,425,431,432,433,434,435,440,441,443,445,447,449,450,45 >>>>>>> 2,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,494 >>>>>>> ,495,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51 >>>>>>> [... truncated] >>>>>>> >>>>>>> 2: In qc.affy(unnormalised, ...) : >>>>>>> CDF Environment name ' hgu95av2cdf ' does not match cdfname ' >>>>>>> >>>>>>> mogene10stv1cdf ' >>>>>>> >>>>>>> Error in plot(qc(object)) : >>>>>>> error in evaluating the argument 'x' in selecting a method for >>>>>>> >>>>>>> function 'plot' >>>>>>> >>>>>>> >>>>>>> This: /Error: NAs in foreign function call (arg 1)/ >>>>>>> >>>>>>> seems to imply that: >>>>>>> - there's an error in the '(arg 1)' but which (arg 1)? >>>>>>> >>>>>>> If this refers to the arg >>>>>>> >>>>>>> /ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf")/ >>>>>>> >>>>>>> then that part of the command seems to complete fine and >>>>>>> returns an >>>>>>> >>>>>>> AffyBatch object as it should >>>>>>> >>>>>>>> str(rawdata) >>>>>>> >>>>>>> Formal class 'AffyBatch' [package "affy"] with 10 slots >>>>>>> >>>>>>> ..@ cdfName : chr "mogene10stv1cdf" >>>>>>> ..@ nrow : int 1050 >>>>>>> ..@ ncol : int 1050 >>>>>>> >>>>>>> /etc/ >>>>>>> >>>>>>> >>>>>>> - or I have NAs in the data, but doesn't point to where or >>>>>>> whether I should address them. >>>>>>> If this is the critical error, I'm guessing I have to choose a >>>>>>> transform that removes or floor-shifts the NAs into a >>>>>>> computational form? >>>>>>> >>>>>>> - the Warnings: >>>>>>> >>>>>>> 1: In data.row.names(row.names, rowsi, i) : >>>>>>> some row.names duplicated: >>>>>>> 4,8,9,13,14,15,16,24,25,26,27,28,29,<almost every="">>>>>>> intervening # omitted> >>>>>>> ,513,515,516,51 [... truncated] >>>>>>> >>>>>>> Would this be related to warning 2 below? >>>>>>> >>>>>>> 2: In qc.affy(unnormalised, ...) : >>>>>>> CDF Environment name ' hgu95av2cdf ' does not match cdfname ' >>>>>>> >>>>>>> mogene10stv1cdf ' >>>>>>> >>>>>>> but if so, what is the proper way to tell QCReport that I'm using >>>>>>> a non-default CDF? >>>>>>> the help section for QCReport doesn't describe any params for >>>>>>> telling it that the CDF env is not 'hgu95av2cdf' and I've tried >>>>>>> including that info in the ReadAffy() fn as noted: >>>>>>> >>>>>>> ie: >>>>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1")) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> sessionInfo() >>>>>>> >>>>>>> R version 2.11.1 (2010-05-31) >>>>>>> i486-pc-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] tools tcltk stats graphics grDevices utils >>>>>>> datasets >>>>>>> [8] methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] makecdfenv_1.26.0 tkWidgets_1.26.0 DynDoc_1.26.0 >>>>>>> [4] widgetTools_1.26.0 hgu95av2cdf_2.6.0 >>>>>>> affydata_1.11.10 [7] affyQCReport_1.26.0 lattice_0.19-11 >>>>>>> RColorBrewer_1.0-2 >>>>>>> >>>>>>> [10] affyPLM_1.24.1 preprocessCore_1.10.0 xtable_1.5-6 >>>>>>> [13] simpleaffy_2.24.0 gcrma_2.20.0 >>>>>>> genefilter_1.30.0 [16] mogene10stv1cdf_2.6.2 affy_1.26.1 >>>>>>> Biobase_2.8.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.16.0 annotate_1.26.1 >>>>>>> AnnotationDbi_1.10.2 [4] Biostrings_2.16.9 DBI_0.2-5 >>>>>>> grid_2.11.1 [7] IRanges_1.6.17 RSQLite_0.9-2 >>>>>>> splines_2.11.1 >>>>>>> >>>>>>> [10] survival_2.35-8 >>>>>>> >>>>>>> >>>>>>> Thanks for your consideration. >>>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> _______________________________________________ >>> 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, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues