Question: Specond with R 3.2.2
0
gravatar for meeta.mistry
3.8 years ago by
meeta.mistry20
United States
meeta.mistry20 wrote:

Hello

I am getting an error with SpeCond code that I had previously run on the same dataset but using R 3.1. I am not sure what is wrong but I wonder if maybe it is version dependent? Especially since the latest branch on GitHub is for 3.1. The error and sessionInfo() is listed below. Thanks very much for any help!

Meeta

 

generalResult <- SpeCond(sub.eset, param.detection=NULL, multitest.correction.method="BH", 
     condition.factor=pData(sub.eset)$neurontype, condition.method='mean',          prefix.file="Ginty", print.hist.pv=FALSE, fit1=NULL, fit2=NULL, specificOutlierStep1=NULL)

 

[1] "The expressionMatrix argument that you entered has been coverted to a matrix using the getMatrixFromExpressionSet() function"
[1] "Step1"
[1] "Step1, fitting"
[1] "start: get null distributions"
[1] "end: get null distributions"
[1] "start: specific detection from p-values"
[1] "end: specific detection from p-values"
[1] "No probe set is selective"
[1] "Step2"
[1] "Step2, fitting"
[1] "start: get null distributions"
Error in names(min_lk_values) = lk_names : 
  'names' attribute [4] must be the same length as the vector [2]
In addition: There were 15 warnings (use warnings() to see them)

 

 

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SpeCond_1.22.0            hwriter_1.3.2             fields_8.2-1              maps_2.3-11               spam_1.0-1               
 [6] mclust_5.0.2              BiocInstaller_1.18.4      vsn_3.36.0                ggdendro_0.1-15           DESeq2_1.8.1             
[11] RcppArmadillo_0.5.500.2.0 Rcpp_0.12.0               GenomicRanges_1.20.6      GenomeInfoDb_1.4.2        IRanges_2.2.7            
[16] S4Vectors_0.6.5           NMF_0.20.6                cluster_2.0.3             rngtools_1.2.4            pkgmaker_0.22            
[21] registry_0.3              RColorBrewer_1.1-2        genefilter_1.50.0         Biobase_2.28.0            BiocGenerics_0.14.0      
[26] gridExtra_2.0.0           rmarkdown_0.8             knitr_1.11                knitrBootstrap_1.0.0      pheatmap_1.0.7           
[31] CHBUtils_0.1              gplots_2.17.0             reshape_0.8.5             ggplot2_1.0.1             edgeR_3.10.2             
[36] limma_3.24.15            

loaded via a namespace (and not attached):
 [1] bitops_1.0-6          doParallel_1.0.8      tools_3.2.2           affyio_1.36.0         rpart_4.1-10          KernSmooth_2.23-15   
 [7] Hmisc_3.16-0          DBI_0.3.1             colorspace_1.2-6      nnet_7.3-11           preprocessCore_1.30.0 formatR_1.2          
[13] labeling_0.3          caTools_1.17.1        scales_0.3.0          affy_1.46.1           stringr_1.0.0         digest_0.6.8         
[19] foreign_0.8-66        XVector_0.8.0         htmltools_0.2.6       highr_0.5             RSQLite_1.0.0         BiocParallel_1.2.20  
[25] gtools_3.5.0          acepack_1.3-3.3       magrittr_1.5          Formula_1.2-1         futile.logger_1.4.1   munsell_0.4.2        
[31] proto_0.3-10          stringi_0.5-5         yaml_2.1.13           MASS_7.3-44           zlibbioc_1.14.0       plyr_1.8.3           
[37] gdata_2.17.0          lattice_0.20-33       splines_3.2.2         annotate_1.46.1       locfit_1.5-9.1        markdown_0.7.7       
[43] geneplotter_1.46.0    reshape2_1.4.1        codetools_0.2-14      futile.options_1.0.0  XML_3.98-1.3          evaluate_0.7.2       
[49] latticeExtra_0.6-26   lambda.r_1.1.7        foreach_1.4.2         gtable_0.1.2          gridBase_0.4-7        mime_0.4             
[55] xtable_1.7-4          survival_2.38-3       iterators_1.0.7       AnnotationDbi_1.30.1 
specond • 626 views
ADD COMMENTlink modified 3.8 years ago by Florence Cavalli50 • written 3.8 years ago by meeta.mistry20

You mention github; did you install the package from github or did you use biocLite() as recommended? Only biocLite() will install the appropriate version of the package for your version of R.

Also do the following to make sure your configuration is valid; if not it will tell you what to do:

library(BiocInstaller)
biocValid()

 

ADD REPLYlink written 3.8 years ago by Dan Tenenbaum8.2k

I installed using biocLite. I was just looking on GitHub to see if there were updates for R 3.2

ADD REPLYlink written 3.8 years ago by meeta.mistry20
Answer: Specond with R 3.2.2
0
gravatar for Florence Cavalli
3.8 years ago by
Florence Cavalli50 wrote:

Hello Meeta,

Could you send me directly a small example dataset that would allow me to reproduce the error. 

Thanks,

Florence

ADD COMMENTlink written 3.8 years ago by Florence Cavalli50
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