Hello,
I am have issues loading in my cuffdiff output into cummeRbund. I'm using cufflinks version 2.2.1 and the most up to date CummeRbund version. I see in other posts that RSQlite might be the problem.The error I'm receiving is:
cuffData <- readCufflinks("458_all_diff", rebuild = T) Creating database 458_all_diff/cuffData.db Reading Run Info File 458_all_diff/run.info Writing runInfo Table Reading Read Group Info 458_all_diff/read_groups.info Writing replicates Table Reading 458_all_diff/genes.fpkm_tracking Checking samples table... Populating samples table... Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Are there any update to date fixes out there or someone who knows how to solve this issue? Any help would be much appreciated as I am trying to obtain some nice visuals like volcano plots for my lab's projects and I'm crunched for time. Any help would be much appreciated.
Bryce
Instead of trying to solve this error, you should instead use the new tuxedo pipeline (hisat + stringtie + ballgown).
If you really want to fix cummeRbund, you have to downgrade it and RSQLite, as described on this post (which you probably did read, I guess), or install the development version, as described on this post.
What is the output of
sessionInfo()?Sorry for the late reply. Here is my sessionInfo
R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] devtools_1.13.5 cummeRbund_2.18.0 Gviz_1.20.0 rtracklayer_1.36.6 GenomicRanges_1.28.6 [6] GenomeInfoDb_1.12.3 IRanges_2.10.5 S4Vectors_0.14.7 fastcluster_1.1.24 reshape2_1.4.3
[11] ggplot2_2.2.1 RSQLite_2.0 BiocGenerics_0.22.1
loaded via a namespace (and not attached): [1] httr_1.3.1 Biobase_2.36.2 AnnotationHub_2.8.3
[4] bit64_0.9-7 splines_3.4.2 shiny_1.0.5
[7] Formula_1.2-2 interactiveDisplayBase_1.14.0 latticeExtra_0.6-28
[10] blob_1.1.0 BSgenome_1.44.2 GenomeInfoDbData_0.99.0
[13] Rsamtools_1.28.0 yaml_2.1.18 pillar_1.2.1
[16] backports_1.1.2 lattice_0.20-35 biovizBase_1.24.0
[19] digest_0.6.15 RColorBrewer_1.1-2 XVector_0.16.0
[22] checkmate_1.8.5 colorspace_1.3-2 httpuv_1.3.6.2
[25] htmltools_0.3.6 Matrix_1.2-12 plyr_1.8.4
[28] pkgconfig_2.0.1 XML_3.98-1.10 biomaRt_2.32.1
[31] zlibbioc_1.22.0 xtable_1.8-2 scales_0.5.0
[34] BiocParallel_1.10.1 htmlTable_1.11.2 tibble_1.4.2
[37] AnnotationFilter_1.0.0 withr_2.1.1 SummarizedExperiment_1.6.5
[40] GenomicFeatures_1.28.5 nnet_7.3-12 lazyeval_0.2.1
[43] mime_0.5 survival_2.41-3 magrittr_1.5
[46] memoise_1.1.0 foreign_0.8-69 BiocInstaller_1.26.1
[49] tools_3.4.2 data.table_1.10.4-3 matrixStats_0.53.1
[52] stringr_1.3.0 munsell_0.4.3 cluster_2.0.6
[55] DelayedArray_0.2.7 ensembldb_2.0.4 AnnotationDbi_1.38.2
[58] Biostrings_2.44.2 compiler_3.4.2 rlang_0.2.0
[61] RCurl_1.95-4.10 dichromat_2.0-0 rstudioapi_0.7
[64] VariantAnnotation_1.22.3 htmlwidgets_1.0 bitops_1.0-6
[67] base64enc_0.1-3 gtable_0.2.0 curl_3.1
[70] DBI_0.8 R6_2.2.2 GenomicAlignments_1.12.2
[73] gridExtra_2.3 knitr_1.20 bit_1.1-12
[76] Hmisc_4.1-1 ProtGenerics_1.8.0 stringi_1.1.7
[79] Rcpp_0.12.15 rpart_4.1-13 acepack_1.4.1