Question: maSigPro: error using see.genes()
0
gravatar for valentine.murigneux
22 months ago by
valentine.murigneux0 wrote:

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

masigpro • 447 views
ADD COMMENTlink modified 12 months ago by therealsisterdot0 • written 22 months ago by valentine.murigneux0
Answer: maSigPro: error using see.genes()
0
gravatar for therealsisterdot
12 months ago by
therealsisterdot0 wrote:

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!

ADD COMMENTlink written 12 months ago by therealsisterdot0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 328 users visited in the last hour