Question: error in ballgown bioconducor package
gravatar for Kritika
3.6 years ago by
Kritika260 wrote:

Hello All

I have 4 samples M1 , M2 , W1, W2 . I have done alignment with Ecoli ref genome usng hisat2 on this sample i ran stringtie for abundance estimation Now i am trying to run ball gown on this sampleas of now i tried this commands:

data_directory <- "/Hisat_stringtie_/string_out/"
bg = ballgown(dataDir=data_directory, samplePattern="string_out_", meas='all')

transcript_fpkm = texpr(bg, 'FPKM')
transcript_cov = texpr(bg, 'cov')
whole_tx_table = texpr(bg, 'all')
exon_mcov = eexpr(bg, 'mcov')
junction_rcount = iexpr(bg)
whole_intron_table = iexpr(bg, 'all')
gene_expression = gexpr(bg)

pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=2))

pheno_data <- pData(bg)



bg_2 = subset(bg,"rowVars(texpr(bg))>1", genomesubset = TRUE )

stat_results = stattest(bg_2, feature='transcript' ,meas='FPKM', covariate='group')

After running stattest i am getting error:

Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[3,3] = 0

please help me i am not able to understand the error .

Where i am getting wrong


R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.10

locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C

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

other attached packages: [1] dplyr_0.5.0 genefilter_1.52.1
[3] BiocStyle_1.8.0 ballgown_2.2.0
[5] Rqc_1.4.2 ggplot2_2.2.0
[7] ShortRead_1.28.0 GenomicAlignments_1.6.3
[9] SummarizedExperiment_1.0.2 Biobase_2.30.0
[11] Rsamtools_1.22.0 GenomicRanges_1.22.4
[13] GenomeInfoDb_1.6.3 Biostrings_2.38.4
[15] XVector_0.10.0 IRanges_2.4.8
[17] S4Vectors_0.8.11 BiocGenerics_0.16.1
[19] BiocParallel_1.4.3

loaded via a namespace (and not attached): [1] splines_3.2.2 GenomicFiles_1.6.2
[3] Formula_1.2-1 shiny_0.14.2
[5] assertthat_0.1 highr_0.6
[7] latticeExtra_0.6-28 BSgenome_1.38.0
[9] RSQLite_1.1 lattice_0.20-34
[11] biovizBase_1.18.0 limma_3.26.9
[13] digest_0.6.10 RColorBrewer_1.1-2
[15] colorspace_1.3-1 htmltools_0.3.5
[17] httpuv_1.3.3 Matrix_1.2-7.1
[19] plyr_1.8.4 XML_3.98-1.5
[21] biomaRt_2.26.1 zlibbioc_1.16.0
[23] xtable_1.8-2 scales_0.4.1
[25] htmlTable_1.7 tibble_1.2
[27] annotate_1.48.0 mgcv_1.8-16
[29] GenomicFeatures_1.22.13 nnet_7.3-12
[31] lazyeval_0.2.0 survival_2.40-1
[33] magrittr_1.5 mime_0.5
[35] evaluate_0.10 memoise_1.0.0
[37] nlme_3.1-128 hwriter_1.3.2
[39] foreign_0.8-67 tools_3.2.2
[41] data.table_1.10.0 stringr_1.1.0
[43] munsell_0.4.3 cluster_2.0.5
[45] AnnotationDbi_1.32.3 lambda.r_1.1.9
[47] futile.logger_1.4.3 grid_3.2.2
[49] RCurl_1.95-4.8 dichromat_2.0-0
[51] VariantAnnotation_1.16.4 labeling_0.3
[53] bitops_1.0-6 gtable_0.2.0
[55] DBI_0.5-1 markdown_0.7.7
[57] reshape2_1.4.2 R6_2.2.0
[59] gridExtra_2.2.1 knitr_1.15.1
[61] rtracklayer_1.30.4 Hmisc_4.0-0
[63] futile.options_1.0.0 stringi_1.1.2
[65] sva_3.18.0 Rcpp_0.12.8
[67] rpart_4.1-10 acepack_1.4.1


rna-seq d.e ball gown • 1.5k views
ADD COMMENTlink modified 3.6 years ago by WouterDeCoster44k • written 3.6 years ago by Kritika260

Hello kritikamish99!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 3.6 years ago by WouterDeCoster44k

sorry for that actually i need to tackle the error at earliest so i posted in support bioconductor the same question i will see that does not happens again

ADD REPLYlink written 3.6 years ago by Kritika260
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