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

[Assa Yeroslaviz]

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/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()


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