Hi All,

I'm trying to use DEXSeq for differential splice variant usage on my SGseq results.

After creating the DEXSeqDataSet and estimated size factor, I continued with dispersion estimation. However, I don't know why it received the following error message. I checked the previous questions regarding the same error I updated my R but couldn't find how to solve it.

dx <- estimateDispersions(dx, formula = FullModel) #Dispersion estimation


Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA) : 
  replacement has 1 row, data has 0

May you please help me to solve it?

Another question to make sure of in my design formula: Am I right with "exon"? Should exon be defined before running DEXseqDataSet, or is it generated after running the DEXSeqDataSet function, and how it defines it?

Many thanks in advance!

Here is my code:

sgvc <- readRDS("sgvc-analyzevariants.rds")
si_complete <- read.csv("si_complete.csv")


sgv.counts <- counts(sgvc) #analogously to per-exon counts
vid <- as.character(variantID(sgvc)) #analogously to exon identifiers
eid <- as.character(variantID(sgvc)) #analogously to gene identifiers

sample_info <- data.frame(sample= si_complete$sample_name, condition=si_complete$condition, Sex=si_complete$Sex, Age= si_complete$Age,PC1= si_complete$PC1, PC2= si_complete$PC2, PC3= si_complete$PC3)


FullModel= ~ sample + exon + condition:exon + Sex:exon+ Age:exon + PC1:exon + PC2:exon + PC3:exon
ReducedModel = ~ sample + exon + Sex:exon+ Age:exon + PC1:exon + PC2:exon + PC3:exon


dx<- DEXSeqDataSet(sgv.counts, featureID = vid, groupID = eid ,sample_info, design = FullModel)

# test for differential exon usage
dx <- estimateSizeFactors(dx) #normalization

dx <- estimateDispersions(dx, formula = FullModel) #Dispersion estimation


Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA) : 
  replacement has 1 row, data has 0

> sessionInfo()

R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19043)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/Paris
tzcode source: internal

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

other attached packages:
 [1] DEXSeq_1.50.0               RColorBrewer_1.1-3          AnnotationDbi_1.66.0        DESeq2_1.44.0               BiocParallel_1.38.0        
 [6] SGSeq_1.38.0                SummarizedExperiment_1.34.0 Biobase_2.64.0              MatrixGenerics_1.16.0       matrixStats_1.3.0          
[11] Rsamtools_2.20.0            Biostrings_2.72.0           XVector_0.44.0              GenomicRanges_1.56.0        GenomeInfoDb_1.40.1        
[16] IRanges_2.38.0              S4Vectors_0.42.0            BiocGenerics_0.50.0        

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1         dplyr_1.1.4              blob_1.2.4               filelock_1.0.3           bitops_1.0-7             fastmap_1.2.0           
 [7] RCurl_1.98-1.14          BiocFileCache_2.12.0     GenomicAlignments_1.40.0 digest_0.6.35            XML_3.99-0.16.1          lifecycle_1.0.4         
[13] statmod_1.5.0            survival_3.6-4           KEGGREST_1.44.0          RSQLite_2.3.7            genefilter_1.86.0        magrittr_2.0.3          
[19] compiler_4.4.0           rlang_1.1.3              progress_1.2.3           tools_4.4.0              igraph_2.0.3             utf8_1.2.4              
[25] yaml_2.3.8               rtracklayer_1.64.0       prettyunits_1.2.0        S4Arrays_1.4.1           bit_4.0.5                curl_5.2.1              
[31] DelayedArray_0.30.1      xml2_1.3.6               abind_1.4-5              hwriter_1.3.2.1          grid_4.4.0               fansi_1.0.6             
[37] xtable_1.8-4             colorspace_2.1-0         ggplot2_3.5.1            scales_1.3.0             biomaRt_2.60.0           cli_3.6.2               
[43] crayon_1.5.2             generics_0.1.3           httr_1.4.7               rjson_0.2.21             RUnit_0.4.33             DBI_1.2.2               
[49] cachem_1.1.0             stringr_1.5.1            splines_4.4.0            zlibbioc_1.50.0          parallel_4.4.0           BiocManager_1.30.23     
[55] restfulr_0.0.15          vctrs_0.6.5              Matrix_1.7-0             jsonlite_1.8.8           geneplotter_1.82.0       hms_1.1.3               
[61] bit64_4.0.5              GenomicFeatures_1.56.0   locfit_1.5-9.9           annotate_1.82.0          glue_1.7.0               codetools_0.2-20        
[67] stringi_1.8.4            gtable_0.3.5             BiocIO_1.14.0            UCSC.utils_1.0.0         munsell_0.5.1            tibble_3.2.1            
[73] pillar_1.9.0             rappdirs_0.3.3           GenomeInfoDbData_1.2.12  dbplyr_2.5.0             R6_2.5.1                 httr2_1.0.1             
[79] lattice_0.22-6           png_0.1-8                memoise_2.0.1            Rcpp_1.0.12              SparseArray_1.4.5        pkgconfig_2.0.3