plotDEXSeq error?
0
0
Entering edit mode
@183232d3
Last seen 17 months 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 • 974 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 781 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6