

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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