Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
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Entering edit mode
dmbergau • 0
@bbbdbca0
Last seen 6 weeks ago
United States

I am working through the Analyzing RNA-seq data with DESeq2 tutorial, and running it through RMarkdown.

Loading the tximeta package in the tutorial code below:

coldata <- samples
coldata$files <- files
coldata$names <- coldata$run

library("tximeta")
# se <- tximeta(coldata)
# ddsTxi <- DESeqDataSet(se, design = ~ condition)

Is causing the following error message:

Error in UseMethod("filter_") : no applicable method for 'filter_' applied to an object of class` `"c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql',` `'tbl_lazy', 'tbl')"

From the win-library DESCRIPTION file the version of tximeta is:

Package: tximeta Version: 1.2.2

Suggestions for how to get past this would be greatly appreciated.

sessionInfo()  
R version 3.6.0 (2019-04-26)  
Platform: i386-w64-mingw32/i386 (32-bit)  
Running under: Windows >= 8 (build 9200)  

Matrix products: default  

locale:  
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C  
[5] LC_TIME=English_United States.1252  

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

loaded via a namespace (and not attached):  
[1] compiler_3.6.0  fastmap_1.1.0   htmltools_0.5.2 tools_3.6.0     yaml_2.2.1      rmarkdown_2.11   
[7] knitr_1.36      xfun_0.28       digest_0.6.29   rlang_0.4.12    evaluate_0.14
tximeta UseMethod("filter_") DESeq2 • 122 views
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Entering edit mode
@mikelove
Last seen 1 hour ago
United States

I'm not sure about that error (tximeta works on the Windows build machines), but is there a reason you need to use an out of date version of Bioconductor? Why not the latest?

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