Dear all,

I have performed a time-course RNA-seq experiment using maSigPro. I have found differentially expressed genes, and now intend to cluster those by their expression pattern over the time. But I got an error when trying to use the function see.genes(), cf below. I should mention that I had a warning message (glm.fit: algorithm did not converge) when running the p.vector() and T.fit() functions.

> see.genes(sigs$sig.genes$BCCvsControl, show.fit = T, dis =design$dis,cluster.method="hclust" ,cluster.data = 1, k = 9)
Error in repvect[1:length(repvect)] - c(0, repvect[1:(length(repvect) -  :
  non-numeric argument to binary operator

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

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=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] dplyr_0.5.0                plyr_1.8.4                
 [3] plotrix_3.6-4              RColorBrewer_1.1-2        
 [5] Hmisc_3.17-4               ggplot2_2.2.1             
 [7] Formula_1.2-1              survival_2.41-3           
 [9] lattice_0.20-35            stringr_1.2.0             
[11] maptools_0.9-2             sp_1.2-4                  
[13] DESeq2_1.14.1              SummarizedExperiment_1.4.0
[15] GenomicRanges_1.26.4       GenomeInfoDb_1.10.3       
[17] IRanges_2.8.2              S4Vectors_0.12.2          
[19] maSigPro_1.48.0            MASS_7.3-45               
[21] Biobase_2.32.0             BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] genefilter_1.56.0    locfit_1.5-9.1       splines_3.3.1       
 [4] colorspace_1.3-2     chron_2.3-47         XML_3.98-1.4        
 [7] foreign_0.8-66       DBI_0.6-1            BiocParallel_1.8.2  
[10] zlibbioc_1.18.0      munsell_0.4.3        gtable_0.2.0        
[13] latticeExtra_0.6-28  geneplotter_1.50.0   AnnotationDbi_1.36.2
[16] Rcpp_0.12.10         acepack_1.4.1        xtable_1.8-2        
[19] scales_0.4.1         annotate_1.52.1      XVector_0.14.1      
[22] gridExtra_2.2.1      stringi_1.1.5        grid_3.3.1          
[25] bitops_1.0-6         tools_3.3.1          magrittr_1.5        
[28] lazyeval_0.2.0       RCurl_1.95-4.8       tibble_1.3.0        
[31] RSQLite_1.0.0        cluster_2.0.4        venn_1.2            
[34] Matrix_1.2-6         data.table_1.9.6     assertthat_0.2.0    
[37] R6_2.2.0             rpart_4.1-10         mclust_5.2.3        
[40] nnet_7.3-12 

Thanks for your help.

Regards,

Valentine Murigneux

hey Valentine,

i got a similar error because the Replicate column in my design matrix was not numeric, and resolved that error with

design$Replicate<-as.numeric(design$Replicate)

repvec is defined in see.genes but the error could be from plotProfiles

best!