[BioC] QCReport: specifying alt CDF (MoGene-1_0-st-v1)?
Martin Morgan
mtmorgan at fhcrc.org
Wed Sep 22 20:34:18 CEST 2010
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/contrib/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.
>>>>
>>>
>>>
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