problem with oneChannelGUI
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Entering edit mode
@annadolnik-9009
Last seen 6.0 years ago
Germany

Dear all,

I encountered a problem with running oneChannelGUI under Windows 7 OS. First I installed Tcl 8.6 / Tk 8.6. Then I installed R. Finally I installed packages using:

source("http://bioconductor.org/biocLite.R")
biocLite(c("Biobase", "limma", "affylmGUI", "tkWidgets", "GOstats", "AnnotationDbi", "preprocessCore", "IRanges", "baySeq", "Rsamtools", "R.utils", "annotate", "genefilter", "maSigPro", "pamr", "pdmclass", "ChIPpeakAnno", "chipseq", "BSgenome", "Rgraphviz", "affy" ,"annaffy", "affyPLM", "multtest", "ssize", "sizepower", "siggenes", "RankProd", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "edgeR",  "metaArray", "MergeMaid", "biomaRt", "GenomeGraphs","AffyCompatible", "Biostrings", "rtracklayer", "Genominator", "hugene10sttranscriptcluster.db", "mogene10sttranscriptcluster.db", "ragene10sttranscriptcluster.db", "HuExExonProbesetLocation", "MoExExonProbesetLocation", "RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund"))

I could open a graphical interface of oneChannelGUI, but when I started a run, I got the following errors:

*error in file(file,"rt"):can not open the connection

*error in grep (target array names [i], names [i], names(my.exons)):object 'my.exons' not found

*error in try(exp,TRUE):object 'my.exons' not found

*error in names(my.exons)<-tmp1.pd$FileName:object 'my.exons' not found

*Error in annotatedDataFrameFrom(expr,byrow=TRUE), error in evaluating the argument 'object' in selecting a method for function....

*Error in validObject(NormalizedArrayData): NormalizedArrayData not found.

I installed an older version of R (3.1.2 from October 2014) and re-installed libraries. I get the same errors. My actual setup is:

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
 [1] splines   stats4    tools     tcltk     parallel  stats     graphics  grDevices utils     datasets 
[11] methods   base     

other attached packages:
 [1] oneChannelGUI_1.32.0                    chimera_1.8.5                          
 [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.18.7                 
 [5] BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.34.1                        
 [7] rtracklayer_1.26.3                      org.Hs.eg.db_3.0.0                     
 [9] RSQLite_1.0.0                           DBI_0.3.1                              
[11] AnnotationDbi_1.28.2                    GenomicAlignments_1.2.2                
[13] siggenes_1.40.0                         multtest_2.22.0                        
[15] Rsamtools_1.18.3                        Biostrings_2.34.1                      
[17] XVector_0.6.0                           GenomicRanges_1.18.4                   
[19] GenomeInfoDb_1.2.5                      IRanges_2.0.1                          
[21] S4Vectors_0.4.0                         tkWidgets_1.44.0                       
[23] DynDoc_1.44.0                           widgetTools_1.44.0                     
[25] affylmGUI_1.40.2                        tkrplot_0.0-23                         
[27] affyPLM_1.42.0                          preprocessCore_1.28.0                  
[29] gcrma_2.38.0                            affy_1.44.0                            
[31] Biobase_2.26.0                          BiocGenerics_0.12.1                    

loaded via a namespace (and not attached):
 [1] affyio_1.34.0        base64enc_0.1-3      BatchJobs_1.6        BBmisc_1.9           BiocInstaller_1.16.5
 [6] BiocParallel_1.0.3   biomaRt_2.22.0       bitops_1.0-6         brew_1.0-6           checkmate_1.6.2     
[11] codetools_0.2-14     digest_0.6.8         fail_1.3             foreach_1.4.3        iterators_1.0.8     
[16] limma_3.22.7         magrittr_1.5         MASS_7.3-44          R2HTML_2.3.1         RCurl_1.95-4.7      
[21] sendmailR_1.2-1      stringi_0.5-5        stringr_1.0.0        survival_2.38-3      XML_3.98-1.3        
[26] xtable_1.7-4         zlibbioc_1.12.0     
> affylmGUIenvironment$aptDir
[1] "C:/DATA/Affymetrix/Affymetrix Power Tools/APT-1.18.0"
> affylmGUIenvironment$libDirLocation
[1] "C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs"

I get the following warning messages:

Warning messages:
1: package ‘tkrplot’ was built under R version 3.1.3 
2: package ‘GenomeInfoDb’ was built under R version 3.1.3 
3: package ‘AnnotationDbi’ was built under R version 3.1.3 
4: package ‘RSQLite’ was built under R version 3.1.3 
5: package ‘DBI’ was built under R version 3.1.3 
6: package ‘rtracklayer’ was built under R version 3.1.3 
7: package ‘GenomicFeatures’ was built under R version 3.1.3 

Gene level probe sets summary started

Gene level probe sets summary ended
Warning messages:
1: running command 'C:/DATA/Affymetrix/Affymetrix Power Tools/APT-1.18.0/bin/apt-probeset-summarize -a rma-sketch -p C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs/HuEx-1_0-st-v2.r2.pgf -c C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs/HuEx-1_0-st-v2.r2.clf -m C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs/HuEx-1_0-st-v2.r2.dt1.hg18.extended.mps -o C:/DATA/ExonArraySet/CELfiles/out1bc0622846de --cel-files C:/DATA/ExonArraySet/CELfiles/target1bc029952282' had status 127 
2: In file(file, "rt") :
  cannot open file 'C:/DATA/ExonArraySet/CELfiles/out1bc0622846de/': No such file or directory

A file target1bc029952282 is generated, but not a directory out1bc0622846de containing output files.

I double checked target file. It is tab-delimited .txt. 

 

I am really greatful for any suggestions. Thank you very much for your help and input!

Kind Regards,

Anna

onechannelgui exon array analysis R • 846 views
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0
Entering edit mode
@raffaele-calogero-294
Last seen 5.9 years ago
Italy/Turin/University of Torino

Dear Anna,

It seems to me a problem due to the presence of space in the path where R is installed:

C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs

You need to locate R in a path without spaces as for example:

C:/R/R-3.1.2/

Let me know if you need further help

Cheers

Raf

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Entering edit mode
@raffaele-calogero-294
Last seen 5.9 years ago
Italy/Turin/University of Torino

Sorry I forgot to tell you that it is better to update R to the latest version, i.e. 3.2.2

Cheers

Raf

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0
Entering edit mode
@annadolnik-9009
Last seen 6.0 years ago
Germany

Dear Raffaele,

thank you very much! I reinstalled R as you indicated, adjusted the path of Affymetrix Power Tools to one without spaces and now can run oneChannelGUI. Thank you very much again for your immediate response!

Best Regards,

Anna 

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