[BioC] strange error message with arrayQualityMetrics

[Wolfgang Huber]

Dear Ying

Something funny is going on with your filesystem.
What is the output of 'getwd()' and 'dir()' after the error is thrown?

	Best wishes
	Wolfgang



Feb/24/12 8:54 PM, ying chen scripsit::
>
>
> Hi guys,
>
> When I ran arrayQualityMetrics, I got a strange error message and no result was generated. I did a similar run with another dataset last night and had no problem. I cannot tell what went wrong today. Any suggestion?
>
> Thanks a lot for the help!
>
> Ying
>
>
>> library("affy")
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'browseVignettes()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation("pkgname")'.
>
>> library("hgu133plus2hsentrezgcdf")
>> mydata<- ReadAffy(cdfname="hgu133plus2hsentrezgcdf")
>> mydata
> AffyBatch object
> size of arrays=1164x1164 features (150 kb)
> cdf=hgu133plus2hsentrezgcdf (18185 affyids)
> number of samples=353
> number of genes=18185
> annotation=hgu133plus2hsentrezgcdf
> notes=
>> hist(mydata)
>> boxplot(mydata,col="red")
>> library("arrayQualityMetrics")
>> arrayQualityMetrics(expressionset=mydata,do.logtransform=TRUE)
> The directory 'arrayQualityMetrics report for mydata' has been created.
> Error in cpSubs(src, dest) :
>    'dest' does not exist, and it cannot be created: arrayQualityMetrics report for mydata
> In addition: Warning message:
> In dir.create(dest) :
>    cannot create dir 'arrayQualityMetrics report for mydata', reason 'No such file or directory'
>>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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] arrayQualityMetrics_3.10.0     hgu133plus2hsentrezgcdf_13.0.0
> [3] affy_1.32.1                    Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.22.0         affyPLM_1.30.0        annotate_1.32.1
>   [4] AnnotationDbi_1.16.17 beadarray_2.4.1       BiocInstaller_1.2.1
>   [7] Biostrings_2.22.0     Cairo_1.5-1           cluster_1.14.2
> [10] DBI_0.2-5             genefilter_1.36.0     grid_2.14.1
> [13] Hmisc_3.9-2           hwriter_1.3           IRanges_1.12.6
> [16] lattice_0.20-0        latticeExtra_0.6-19   limma_3.10.2
> [19] preprocessCore_1.16.0 RColorBrewer_1.0-5    RSQLite_0.11.1
> [22] setRNG_2009.11-1      splines_2.14.1        survival_2.36-12
> [25] SVGAnnotation_0.9-0   tcltk_2.14.1          tools_2.14.1
> [28] vsn_3.22.0            XML_3.9-4             xtable_1.7-0
> [31] zlibbioc_1.0.0
>>
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber