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 

Hello Meeta,

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

Thanks,

Florence