[BioC] QCReport: specifying alt CDF (MoGene-1_0-st-v1)?
James W. MacDonald
jmacdon at med.umich.edu
Tue Sep 21 23:08:39 CEST 2010
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.
>
--
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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