DEXSeq estimateDispersions - Error in `$<`(`*tmp*`, "dispersion", value = NA)
Entering edit mode
Sara • 0
Last seen 18 hours ago

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

May you please help me to solve 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 `$<`(`*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

[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
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