plotDEXSeq error?
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Entering edit mode
@183232d3
Last seen 1 day ago
Czechia

Hi I have a standard condition KO vs WT and i want to know the exon usage in KO condition. So i used following script

Code should be placed in three backticks as shown below


my_gtf_1 <- makeTxDbFromEnsembl(organism="Homo sapiens",
                    release=86,
                    circ_seqs=NULL,
                    server="ensembldb.ensembl.org",
                    username="anonymous", password=NULL, port=0L,
                    tx_attrib=NULL)

nonOverlappingExons <- disjointExons(my_gtf_1)

names(nonOverlappingExons) <- paste(mcols(nonOverlappingExons)$gene_id, mcols(nonOverlappingExons)$exonic_part,sep = "_")

Exon_counts<- summarizeOverlaps(nonOverlappingExons,myBams,ignore.strand = FALSE,inter.feature=FALSE)

ToFilter <- apply(assay(Exon_counts),1,function(x) sum(x > 20)) >= 2

Exon_counts_filtered <- Exon_counts[ToFilter, ]

countMatrix <- assay(Exon_counts_filtered)
countGRanges <- rowRanges(Exon_counts_filtered)
geneIDs <- as.vector(unlist(countGRanges$gene_id))
exonIDs <- rownames(countMatrix)
metaData <- data.frame(condition=c("KO","KO","KO","WT","WT","WT"),row.names=colnames(Exon_counts_filtered))


ddx_1 <- DEXSeqDataSet(countMatrix,metaData,design = ~sample+exon+condition:exon,featureID = exonIDs,groupID = geneIDs)
ddx_1 <- estimateSizeFactors(ddx_1)
ddx_1 <- estimateDispersions(ddx_1)
dxd_1 <- testForDEU(ddx_1)
dxd_1 = estimateExonFoldChanges(dxd_1, fitExpToVar="condition")
dxr = DEXSeqResults(dxd_1)
plotDEXSeq( dxr, "ENSG00000000003", legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 )

**Error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : 
need finite 'ylim' values**


groupID         featureID exonBaseMean   dispersion       stat     pvalue      padj       KO       WT log2fold_WT_KO
ENSG00000000003:ENSG00000000003_1 ENSG00000000003 ENSG00000000003_1     237.7838 0.0154993268 3.18606743 0.07426848 0.8995720 21.72677 24.30731     0.37330829
ENSG00000000003:ENSG00000000003_2 ENSG00000000003 ENSG00000000003_2    2697.1990 0.0009817991 0.28744737 0.59186098 0.9596296 55.15708 54.95249    -0.01900645
ENSG00000000003:ENSG00000000003_3 ENSG00000000003 ENSG00000000003_3     756.8533 0.0007919755 0.32614792 0.56793618 0.9571905 36.65145 36.44270    -0.02256554
ENSG00000000003:ENSG00000000003_5 ENSG00000000003 ENSG00000000003_5     568.3346 0.0009387741 0.23865462 0.62517951 0.9625576 32.66184 33.04087     0.04335657
ENSG00000000003:ENSG00000000003_6 ENSG00000000003 ENSG00000000003_6     345.2394 0.0013624177 3.03196976 0.08163885 0.9114054 26.33814 27.56497     0.15860971
ENSG00000000003:ENSG00000000003_7 ENSG00000000003 ENSG00000000003_7     334.3815 0.0025486393 0.02785648 0.86744669 0.9887713 26.45660 26.69058     0.03053553
                                  genomicData countData.SRR1039508_KO_1_Aligned.sortedByCoord.out.bam
ENSG00000000003:ENSG00000000003_1                                                                                                          271

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib


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

other attached packages:
 [1] dplyr_1.0.10                           DEXSeq_1.38.0                         
 [3] RColorBrewer_1.1-3                     DESeq2_1.32.0                         
 [5] BiocParallel_1.26.2                    GenomicAlignments_1.28.0              
 [7] SummarizedExperiment_1.22.0            MatrixGenerics_1.4.3                  
 [9] matrixStats_0.62.0                     BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000
[11] BSgenome_1.60.0                        rtracklayer_1.52.1                    
[13] GenomicFeatures_1.44.2                 AnnotationDbi_1.54.1                  
[15] Biobase_2.52.0                         Rsamtools_2.8.0                       
[17] Biostrings_2.60.2                      XVector_0.32.0                        
[19] GenomicRanges_1.44.0                   GenomeInfoDb_1.28.4                   
[21] IRanges_2.26.0                         S4Vectors_0.30.2                      
[23] BiocGenerics_0.38.0                    DRIMSeq_1.20.0                        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7           lubridate_1.9.0        bit64_4.0.5            filelock_1.0.2        
 [5] progress_1.2.2         httr_1.4.4             tools_4.1.2            utf8_1.2.2            
 [9] R6_2.5.1               DBI_1.1.3              colorspace_2.0-3       withr_2.5.0           
[13] tidyselect_1.2.0       prettyunits_1.1.1      bit_4.0.5              curl_4.3.3            
[17] compiler_4.1.2         cli_3.4.1              xml2_1.3.3             DelayedArray_0.18.0   
[21] scales_1.2.1           genefilter_1.74.1      rappdirs_0.3.3         stringr_1.4.1         
[25] digest_0.6.30          rmarkdown_2.18         pkgconfig_2.0.3        htmltools_0.5.3       
[29] dbplyr_2.2.1           fastmap_1.1.0          limma_3.48.3           RMariaDB_1.2.2        
[33] rlang_1.0.6            rstudioapi_0.14        RSQLite_2.2.18         BiocIO_1.2.0          
[37] generics_0.1.3         hwriter_1.3.2.1        RCurl_1.98-1.9         magrittr_2.0.3        
[41] GenomeInfoDbData_1.2.6 Matrix_1.5-3           Rcpp_1.0.9             munsell_0.5.0         
[45] fansi_1.0.3            lifecycle_1.0.3        stringi_1.7.8          yaml_2.3.6            
[49] edgeR_3.34.1           zlibbioc_1.38.0        plyr_1.8.8             BiocFileCache_2.0.0   
[53] grid_4.1.2             blob_1.2.3             crayon_1.5.2           lattice_0.20-45       
[57] splines_4.1.2          annotate_1.70.0        hms_1.1.2              KEGGREST_1.32.0       
[61] locfit_1.5-9.6         knitr_1.40             pillar_1.8.1           rjson_0.2.21          
[65] geneplotter_1.70.0     reshape2_1.4.4         biomaRt_2.48.3         XML_3.99-0.12         
[69] glue_1.6.2             evaluate_0.18          png_0.1-7              vctrs_0.5.1           
[73] gtable_0.3.1           assertthat_0.2.1       cachem_1.0.6           ggplot2_3.4.0         
[77] xfun_0.35              xtable_1.8-4           restfulr_0.0.15        survival_3.4-0        
[81] tibble_3.1.8           memoise_2.0.1          timechange_0.1.1       statmod_1.4.37        
[85] ellipsis_0.3.2

My DEXSeq final table looks fine

table( dxr$padj < 0.05 ) 
 FALSE   TRUE 
 323011    777 

But still i'm getting this error which i have no clue?

DEXSeq dex • 113 views
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Entering edit mode

Could you share dput(dxr[dxr$groupID=="ENSG00000000003",]) to make your issue reproducible please ? Thanks

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