[BioC] QCReport: specifying alt CDF (MoGene-1_0-st-v1)?

James W. MacDonald jmacdon at med.umich.edu
Wed Sep 22 21:22:14 CEST 2010


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/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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>>>
>>>
>>>      [[alternative HTML version deleted]]
>>>
>>>
>>>
>>>
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>>
>

-- 
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
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