error: Error in H %*% t(dat) : non-conformable arguments

Hi everyone,

Im using the hisat2-stringtie pipeline for my analysis and then isoformswictanalyzer to fix all the MSTRG tags. Im facing an error that i have never encountered before and i can't seem to understand where im going wrong. Im still a beginner and any help will be appreciated.

### Import StringTie Expression data
stringTieQuant <- importIsoformExpression(parentDir ="/stringtie/GH_ballgown_msu7/",readLength=150)

myDesign = data.frame(sampleID = c("GH1BM_R1","GH1BM_R2","GH1BM_R3","GH1NC_R1","GH1NC_R2","GH1NC_R2"),
                      condition = c("BM","BM","BM","NC","NC","NC"))

switchAnalyzeRlist <- importRdata(
    isoformCountMatrix   = stringTieQuant$counts,
    isoformRepExpression = stringTieQuant$abundance,
    designMatrix         = myDesign,
    isoformExonAnnoation = "/stringtie/msu7_merged.gtf",
)

myDesign sampleID condition 1 GH1BM_R1 BM 2 GH1BM_R2 BM 3 GH1BM_R3 BM 4 GH1NC_R1 NC 5 GH1NC_R2 NC 6 GH1NC_R2 NC

OUTPUT: Step 1 of 10: Checking data... Step 2 of 10: Obtaining annotation... importing GTF (this may take a while)... 6695 ( 7.65%) isoforms were removed since they were not expressed in any samples. Step 3 of 10: Fixing StringTie gene annoation problems... 13604 isoforms were assigned the ref_gene_id and gene_name of their associated gene_id. This was only done when the parent gene_id were associated with a single ref_gene_id/gene_name. 3155 isoforms were assigned the ref_gene_id and gene_name of the most similar annotated isoform (defined via overlap in genomic exon coordinates). This was only done if the overlap met the requriements indicated by the three fixStringTieViaOverlap arguments. We were unable to assign 270 isoforms (located within annotated genes) to a known ref_gene_id/gene_name. These were removed to enable analysis of the rest of the isoform from within the merged genes. 1430 gene_ids which were associated with multiple ref_gene_id/gene_names were split into mutliple genes via their ref_gene_id/gene_names. 28749 genes_id were assigned their original gene_id instead of the StringTie gene_id. This was only done when it could be done unambiguous. Step 4 of 10: Calculating expression estimates from count data... Skipped as user supplied expression via the "isoformRepExpression" argument... Step 5 of 10: Testing for unwanted effects... Error in H %% t(dat) : non-conformable arguments

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/combio7/anaconda3/envs/tophat/lib/libopenblasp-r0.3.23.so;  LAPACK version 3.11.0

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       

time zone: Asia/Kuala_Lumpur
tzcode source: system (glibc)

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

other attached packages:
 [1] IsoformSwitchAnalyzeR_2.0.1 pfamAnalyzeR_1.0.1         
 [3] dplyr_1.1.2                 stringr_1.5.0              
 [5] readr_2.1.4                 ggplot2_3.4.2              
 [7] sva_3.49.0                  genefilter_1.83.1          
 [9] mgcv_1.9-0                  nlme_3.1-163               
[11] satuRn_1.8.0                DEXSeq_1.46.0              
[13] RColorBrewer_1.1-3          AnnotationDbi_1.63.2       
[15] DESeq2_1.40.2               SummarizedExperiment_1.31.1
[17] GenomicRanges_1.53.1        GenomeInfoDb_1.37.2        
[19] IRanges_2.35.2              S4Vectors_0.39.1           
[21] MatrixGenerics_1.13.1       matrixStats_1.0.0          
[23] Biobase_2.61.0              BiocGenerics_0.47.0        
[25] BiocParallel_1.35.3         limma_3.57.7               

loaded via a namespace (and not attached):
  [1] jsonlite_1.8.7                tximport_1.28.0              
  [3] magrittr_2.0.3                GenomicFeatures_1.53.1       
  [5] BiocIO_1.11.0                 zlibbioc_1.47.0              
  [7] vctrs_0.6.3                   locfdr_1.1-8                 
  [9] memoise_2.0.1                 Rsamtools_2.17.0             
 [11] RCurl_1.98-1.12               htmltools_0.5.6              
 [13] S4Arrays_1.1.5                progress_1.2.2               
 [15] AnnotationHub_3.8.0           lambda.r_1.2.4               
 [17] curl_5.0.1                    SparseArray_1.1.11           
 [19] plyr_1.8.8                    futile.options_1.0.1         
 [21] cachem_1.0.8                  GenomicAlignments_1.37.0     
 [23] mime_0.12                     lifecycle_1.0.3              
 [25] pkgconfig_2.0.3               Matrix_1.6-0                 
 [27] R6_2.5.1                      fastmap_1.1.1                
 [29] GenomeInfoDbData_1.2.10       shiny_1.7.4.1                
 [31] digest_0.6.33                 colorspace_2.1-0             
 [33] tximeta_1.18.1                geneplotter_1.78.0           
 [35] RSQLite_2.3.1                 hwriter_1.3.2.1              
 [37] filelock_1.0.2                fansi_1.0.4                  
 [39] httr_1.4.6                    abind_1.4-5                  
 [41] compiler_4.3.1                bit64_4.0.5                  
 [43] withr_2.5.0                   DBI_1.1.3                    
 [45] biomaRt_2.57.1                rappdirs_0.3.3               
 [47] DelayedArray_0.27.10          rjson_0.2.21                 
 [49] tools_4.3.1                   interactiveDisplayBase_1.38.0
 [51] httpuv_1.6.11                 glue_1.6.2                   
 [53] VennDiagram_1.7.3             restfulr_0.0.15              
 [55] promises_1.2.1                grid_4.3.1                   
 [57] reshape2_1.4.4                generics_0.1.3               
 [59] gtable_0.3.3                  BSgenome_1.69.0              
 [61] tzdb_0.4.0                    tidyr_1.3.0                  
 [63] ensembldb_2.25.0              hms_1.1.3                    
 [65] xml2_1.3.5                    utf8_1.2.3                   
 [67] XVector_0.41.1                BiocVersion_3.17.1           
 [69] pillar_1.9.0                  vroom_1.6.3                  
 [71] later_1.3.1                   splines_4.3.1                
 [73] BiocFileCache_2.9.1           lattice_0.21-8               
 [75] survival_3.5-5                rtracklayer_1.61.0           
 [77] bit_4.0.5                     annotate_1.79.0              
 [79] tidyselect_1.2.0              locfit_1.5-9.8               
 [81] Biostrings_2.69.2             pbapply_1.7-2                
 [83] gridExtra_2.3                 ProtGenerics_1.33.1          
 [85] edgeR_3.43.8                  futile.logger_1.4.3          
 [87] statmod_1.5.0                 stringi_1.7.12               
 [89] lazyeval_0.2.2                yaml_2.3.7                   
 [91] boot_1.3-28.1                 codetools_0.2-19             
 [93] tcltk_4.3.1                   tibble_3.2.1                 
 [95] BiocManager_1.30.22           cli_3.6.1                    
 [97] xtable_1.8-4                  munsell_0.5.0                
 [99] Rcpp_1.0.11                   dbplyr_2.3.3                 
[101] png_0.1-8                     XML_3.99-0.14                
[103] parallel_4.3.1                ellipsis_0.3.2               
[105] blob_1.2.4                    prettyunits_1.1.1            
[107] AnnotationFilter_1.25.0       bitops_1.0-7                 
[109] scales_1.2.1                  purrr_1.0.2                  
[111] crayon_1.5.2                  rlang_1.1.1                  
[113] KEGGREST_1.41.0               formatR_1.14

kvittingseerup / IsoformSwitchAnalyzeR

error: Error in H %*% t(dat) : non-conformable arguments #218