DRIMSeq + dmFilter
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Entering edit mode
Gaia • 0
@gaia-25069
Last seen 13 months ago
United States

Hello,

I am using DRIMSeq to conduct differential splicing analyses from RNAseq data run with Salmon. unfortunately, I have encountered the below problem. It seems like there are issues with the filtering function. I have tried different parameters but even the simple 0 (meaning no filtering at all) given an error.

Any help and appreciation on how to overcome this is welcome. Thanks, Gaia

> d
#An object of class dmDSdata 
#with 24916 genes and 6 samples
#* data accessors: counts(), samples()
> n <- 6
> n.small <- 1
> d <- dmFilter(d,
+               min_samps_feature_expr=n.small, min_feature_expr=1,
+               min_samps_feature_prop=n.small, min_feature_prop=0.1,
+               min_samps_gene_expr=n, min_gene_expr=1)
#Error in dmDS_filter(counts = x@counts, min_samps_gene_expr = min_samps_gene_expr,  : 
#  !No genes left after filtering!
> n <- 0
> n.small <- 0
> d <- dmFilter(d,
+               min_samps_feature_expr=n.small, min_feature_expr=1,
+               min_samps_feature_prop=n.small, min_feature_prop=0.1,
+               min_samps_gene_expr=n, min_gene_expr=1)
#Error in dmDS_filter(counts = x@counts, min_samps_gene_expr = min_samps_gene_expr,  : 
#  !No genes left after filtering!
> sessionInfo( )
> sessionInfo( )
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /bifx/apps/spack/spack-20190717/opt/spack/linux-centos7-x86_64/gcc-8.2.0/r-3.5.1-sgjamjmaepz56jr3vyephqqefmesazby/rlib/R/lib/libRblas.so
LAPACK: /bifx/apps/spack/spack-20190717/opt/spack/linux-centos7-x86_64/gcc-8.2.0/r-3.5.1-sgjamjmaepz56jr3vyephqqefmesazby/rlib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] GenomicFeatures_1.34.1      EnhancedVolcano_1.0.1       ggrepel_0.8.0               ggplot2_3.1.0               dplyr_1.0.5                
 [6] biobroom_1.14.0             broom_0.5.1                 dbplyr_1.3.0                pheatmap_1.0.12             annotables_0.1.91          
[11] DEXSeq_1.28.3               RColorBrewer_1.1-2          AnnotationDbi_1.44.0        DESeq2_1.22.2               SummarizedExperiment_1.12.0
[16] DelayedArray_0.8.0          matrixStats_0.54.0          GenomicRanges_1.34.0        GenomeInfoDb_1.18.1         IRanges_2.16.0             
[21] S4Vectors_0.20.1            Biobase_2.42.0              BiocGenerics_0.28.0         BiocParallel_1.16.5         DRIMSeq_1.10.1             

loaded via a namespace (and not attached):
 [1] colorspace_1.4-0         hwriter_1.3.2            ellipsis_0.3.1           htmlTable_1.13.1         XVector_0.22.0          
 [6] base64enc_0.1-3          rstudioapi_0.9.0         bit64_0.9-7              fansi_0.4.0              splines_3.5.1           
[11] geneplotter_1.60.0       knitr_1.21               Formula_1.2-3            Rsamtools_1.34.0         annotate_1.60.0         
[16] cluster_2.0.7-1          compiler_3.5.1           httr_1.4.0               backports_1.1.3          assertthat_0.2.0        
[21] Matrix_1.2-15            lazyeval_0.2.1           limma_3.38.3             cli_1.1.0                acepack_1.4.1           
[26] htmltools_0.3.6          prettyunits_1.0.2        tools_3.5.1              gtable_0.2.0             glue_1.4.1.9000         
[31] GenomeInfoDbData_1.2.0   reshape2_1.4.3           Rcpp_1.0.0               vctrs_0.3.6              Biostrings_2.50.2       
[36] nlme_3.1-137             rtracklayer_1.42.1       xfun_0.4                 stringr_1.3.1            lifecycle_1.0.0         
[41] statmod_1.4.32           XML_3.98-1.16            edgeR_3.24.3             zlibbioc_1.28.0          scales_1.0.0            
[46] hms_0.4.2                yaml_2.2.0               memoise_1.1.0            gridExtra_2.3            biomaRt_2.38.0          
[51] rpart_4.1-13             latticeExtra_0.6-28      stringi_1.2.4            RSQLite_2.1.1            genefilter_1.64.0       
[56] checkmate_1.9.0          rlang_0.4.10             pkgconfig_2.0.2          bitops_1.0-6             lattice_0.20-35         
[61] purrr_0.3.4              GenomicAlignments_1.18.1 htmlwidgets_1.3          bit_1.1-14               tidyselect_1.1.0        
[66] plyr_1.8.4               magrittr_1.5             R6_2.3.0                 generics_0.0.2           Hmisc_4.1-1             
[71] DBI_1.0.0                pillar_1.5.1             foreign_0.8-70           withr_2.1.2              survival_2.42-3         
[76] RCurl_1.95-4.11          nnet_7.3-12              tibble_3.1.0             crayon_1.3.4             utf8_1.1.4              
[81] progress_1.2.0           locfit_1.5-9.1           grid_3.5.1               data.table_1.12.0        blob_1.1.1              
[86] digest_0.6.18            xtable_1.8-3             tidyr_0.8.2              munsell_0.5.0
DEXSeq DRIMSeq • 337 views
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Entering edit mode
@mikelove
Last seen 20 hours ago
United States

Examine the counts you are inputting to the functions. It says there are now features where 6 samples have a count of 1 (I guess this is one filter being triggered).

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Entering edit mode

Mike, Sorry, I realized I was stupidity taking only the longer transcript. All is working now - apologies for the trouble!

Gaia

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