Hi,

I followed through the cufflink-cuffdiff-cummerbund pipeline for my analysis involving 2 groups (hyp-has 2 replicate, lyp-only one sample). Everything went well up to cuffdiff but when i tried plotting on cummerbund i end up with error everytime i try to plot (csScatter, csDensity, heatmap) only for the significant genes . Error says that: error:unable to find an inherited method for function 'csScatter' for signature '"data.frame". Im trying to understand where im going wrong, any help will be much appreciated.

Code should be placed in three backticks as shown below

> cuffdiff_data
CuffSet instance with:
     2 samples
     56245 genes
     88197 isoforms
     76870 TSS
     40736 CDS
     56245 promoters
     76870 splicing
     39033 relCDS
> sig_gene_diff <- subset(gene_diff, (significant == 'yes'))
> csScatter(sig_gene_diff, 'hyp', 'lyp')

# Error in (function (classes, fdef, mtable)  : unable to find an inherited method for function 'csScatter' for signature '"data.frame"'

sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/combio7/anaconda3/lib/libopenblasp-r0.3.21.so

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

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

other attached packages:
 [1] cummeRbund_2.36.0    Gviz_1.38.0          rtracklayer_1.54.0  
 [4] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1  IRanges_2.28.0      
 [7] S4Vectors_0.32.4     fastcluster_1.2.3    reshape2_1.4.4      
[10] ggplot2_3.4.2        RSQLite_2.3.0        BiocGenerics_0.40.0 

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.26.0         bitops_1.0-7               
  [3] matrixStats_0.63.0          bit64_4.0.5                
  [5] filelock_1.0.2              RColorBrewer_1.1-3         
  [7] progress_1.2.2              httr_1.4.6                 
  [9] tools_4.1.1                 backports_1.4.1            
 [11] utf8_1.2.3                  R6_2.5.1                   
 [13] rpart_4.1.19                lazyeval_0.2.2             
 [15] Hmisc_5.1-0                 DBI_1.1.3                  
 [17] colorspace_2.1-0            nnet_7.3-19                
 [19] withr_2.5.0                 tidyselect_1.2.0           
 [21] gridExtra_2.3               prettyunits_1.1.1          
 [23] bit_4.0.5                   curl_4.3.3                 
 [25] compiler_4.1.1              cli_3.6.1                  
 [27] Biobase_2.54.0              htmlTable_2.4.1            
 [29] xml2_1.3.4                  DelayedArray_0.20.0        
 [31] labeling_0.4.2              scales_1.2.1               
 [33] checkmate_2.2.0             rappdirs_0.3.3             
 [35] stringr_1.5.0               digest_0.6.31              
 [37] Rsamtools_2.10.0            foreign_0.8-84             
 [39] rmarkdown_2.21              XVector_0.34.0             
 [41] dichromat_2.0-0.1           htmltools_0.5.5            
 [43] base64enc_0.1-3             jpeg_0.1-10                
 [45] pkgconfig_2.0.3             MatrixGenerics_1.6.0       
 [47] ensembldb_2.18.1            dbplyr_2.3.2               
 [49] fastmap_1.1.1               BSgenome_1.62.0            
 [51] htmlwidgets_1.5.4           rlang_1.1.1                
 [53] rstudioapi_0.14             farver_2.1.1               
 [55] BiocIO_1.4.0                generics_0.1.3             
 [57] BiocParallel_1.28.3         dplyr_1.1.2                
 [59] VariantAnnotation_1.40.0    RCurl_1.98-1.12            
 [61] magrittr_2.0.3              GenomeInfoDbData_1.2.7     
 [63] Formula_1.2-5               Matrix_1.5-4.1             
 [65] Rcpp_1.0.10                 munsell_0.5.0              
 [67] fansi_1.0.4                 lifecycle_1.0.3            
 [69] stringi_1.7.12              yaml_2.3.7                 
 [71] SummarizedExperiment_1.24.0 zlibbioc_1.40.0            
 [73] plyr_1.8.8                  BiocFileCache_2.2.1        
 [75] blob_1.2.4                  parallel_4.1.1             
 [77] crayon_1.5.2                lattice_0.21-8             
 [79] Biostrings_2.62.0           GenomicFeatures_1.46.5     
 [81] hms_1.1.3                   KEGGREST_1.34.0            
 [83] knitr_1.43                  pillar_1.9.0               
 [85] rjson_0.2.21                biomaRt_2.50.3             
 [87] XML_3.99-0.14               glue_1.6.2                 
 [89] evaluate_0.21               biovizBase_1.42.0          
 [91] latticeExtra_0.6-29         data.table_1.14.8          
 [93] png_0.1-8                   vctrs_0.6.2                
 [95] gtable_0.3.3                cachem_1.0.8               
 [97] xfun_0.39                   AnnotationFilter_1.18.0    
 [99] restfulr_0.0.15             tibble_3.2.1               
[101] GenomicAlignments_1.30.0    AnnotationDbi_1.56.2       
[103] memoise_2.0.1               cluster_2.1.4

The simplest answer is to point to the error message. The csScatter function doesn't know what to do with a data.frame. But why do you have a data.frame to begin with? There isn't a subset function defined in cummerbund, so when you are subsetting it is likely defaulting to a more general method and not doing the right thing. So ideally you would not use subset and just use your original object.

Also, you are using very old tools. You should upgrade to the current version of R and Bioconductor, as we technically don't support old versions.