Specond with R 3.2.2
1
0
Entering edit mode
meeta.mistry ▴ 20
@meetamistry-7355
Last seen 11 weeks ago
United States

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 • 816 views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
@florence-cavalli-4588
Last seen 6.1 years ago

Hello Meeta,

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

Thanks,

Florence

ADD COMMENT

Login before adding your answer.

Traffic: 570 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6