Hi all,

I have a condition like KO vs WT three replicates for each condition and paired end data. I want to use the DExSEQ for exon usage but i'm getting warning which i don't find the answer yet? Why it is happening? do i have to dig something further?

dxd_1 = DEXSeqDataSetFromFeatureCounts(countFiles_1 , sampleData=sampleTable_1,design= ~ sample + exon + condition:exon,flattenedfile=flattenedFile )

ToFilter_1 <- apply(assay(dxd_1),1,function(x) sum(x > 20)) >= 2
dxd_filtered_1 <- dxd_1[ToFilter_1, ]

dxd_filtered_1 = estimateSizeFactors( dxd_filtered_1 )
dxd_filtered_1 = estimateDispersions( dxd_filtered_1 )
dxd_filtered_1 = testForDEU( dxd_filtered_1 )
dxd_filtered_1 = estimateExonFoldChanges( dxd_filtered_1, fitExpToVar="condition")
dxr2 = DEXSeqResults( dxd_filtered_1 )

warning
# Fit for gene/exon ENSG00000_onegene threw the next warning(s): Too much damping - convergence tolerance not achievable
# Fit for gene/exon ENSG00000something+ENSG00000something1 threw the next warning(s): the matrix is either rank-deficient or indefinite

sessionInfo( )
attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DEXSeq_1.42.0               RColorBrewer_1.1-3          AnnotationDbi_1.58.0        DESeq2_1.36.0              
 [5] SummarizedExperiment_1.26.1 GenomicRanges_1.48.0        GenomeInfoDb_1.32.4         IRanges_2.30.1             
 [9] S4Vectors_0.34.0            MatrixGenerics_1.8.1        matrixStats_0.62.0          Biobase_2.56.0             
[13] BiocGenerics_0.42.0         BiocParallel_1.30.4         dplyr_1.0.10               

loaded via a namespace (and not attached):
 [1] httr_1.4.4             pkgload_1.3.2          bit64_4.0.5            splines_4.2.1          assertthat_0.2.1      
 [6] statmod_1.4.37         BiocFileCache_2.4.0    blob_1.2.3             Rsamtools_2.12.0       GenomeInfoDbData_1.2.8
[11] progress_1.2.2         yaml_2.3.5             pillar_1.8.1           RSQLite_2.2.18         lattice_0.20-45       
[16] glue_1.6.2             digest_0.6.29          XVector_0.36.0         colorspace_2.0-3       htmltools_0.5.3       
[21] Matrix_1.5-3           XML_3.99-0.12          pkgconfig_2.0.3        biomaRt_2.52.0         genefilter_1.78.0     
[26] zlibbioc_1.42.0        xtable_1.8-4           scales_1.2.1           tibble_3.1.8           annotate_1.74.0       
[31] KEGGREST_1.36.3        generics_0.1.3         ggplot2_3.4.0          ellipsis_0.3.2         cachem_1.0.6          
[36] cli_3.4.1              survival_3.4-0         magrittr_2.0.3         crayon_1.5.2           memoise_2.0.1         
[41] evaluate_0.18          fansi_1.0.3            xml2_1.3.3             hwriter_1.3.2.1        prettyunits_1.1.1     
[46] tools_4.2.1            hms_1.1.2              lifecycle_1.0.3        stringr_1.4.1          munsell_0.5.0         
[51] locfit_1.5-9.6         DelayedArray_0.22.0    Biostrings_2.64.1      compiler_4.2.1         rlang_1.0.6           
[56] grid_4.2.1             RCurl_1.98-1.9         rstudioapi_0.14        rappdirs_0.3.3         bitops_1.0-7          
[61] rmarkdown_2.18         gtable_0.3.1           codetools_0.2-18       curl_4.3.3             DBI_1.1.3             
[66] R6_2.5.1               knitr_1.41             fastmap_1.1.0          bit_4.0.4              utf8_1.2.2            
[71] filelock_1.0.2         stringi_1.7.8          parallel_4.2.1         Rcpp_1.0.9             vctrs_0.5.0           
[76] geneplotter_1.74.0     png_0.1-7              dbplyr_2.2.1           tidyselect_1.2.0       xfun_0.34