Hi all,

I am just getting started with RNAseq DE analyses. I processed my data using sailfish and would like to use DESeq2 to further process the results. Here is a snippet of my code

library('tximport')
library('DESeq2')

sf_dirs <- dir()     

files = paste(sf_dirs, 'quant.sf', sep = '/')

tx2gene = read.table('ecoli_transcript_to_gene_mapping.txt', header = FALSE, stringsAsFactors = FALSE, sep = '\t')

data = tximport(files, type = "sailfish", tx2gene = tx2gene)

metadata = read.table('metadata.txt', header = TRUE, stringsAsFactors = FALSE, sep = '\t', row.names = 1)
colnames(metadata) = c('genotype', 'timing')

# set up the DESeq2 object
model <- "~ genotype"    

dds <- DESeqDataSetFromTximport(data, colData = metadata, design = model)

Unfortunately, when I run the last line, I get the following error message:

Error: $ operator is invalid for atomic vectors


My tximport object looks like this:


> str(data)
List of 4
 $ abundance          : num [1:4325, 1:12] 0 1028.1 623.6 1086.6 62.5 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:4325] "b0001" "b0002" "b0003" "b0004" ...
  .. ..$ : NULL
 $ counts             : num [1:4325, 1:12] 0 331.01 65.01 168.01 1.01 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:4325] "b0001" "b0002" "b0003" "b0004" ...
  .. ..$ : NULL
 $ length             : num [1:4325, 1:12] 24.9 2262.6 732.6 1086.6 113.6 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:4325] "b0001" "b0002" "b0003" "b0004" ...
  .. ..$ : NULL
 $ countsFromAbundance: chr "no"



> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.14.0              SummarizedExperiment_1.4.0 Biobase_2.34.0             GenomicRanges_1.26.1      
 [5] GenomeInfoDb_1.10.0        IRanges_2.8.0              S4Vectors_0.12.0           BiocGenerics_0.20.0       
 [9] tximport_1.2.0             BiocInstaller_1.24.0       shiny_0.14.2               wasabi_0.1                
[13] sleuth_0.28.1              dplyr_0.5.0                ggplot2_2.1.0             

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1       Rcpp_0.12.7          lattice_0.20-33      tidyr_0.6.0          assertthat_0.1      
 [6] digest_0.6.10        mime_0.5             R6_2.2.0             plyr_1.8.4           chron_2.3-47        
[11] acepack_1.4.1        RSQLite_1.0.0        zlibbioc_1.20.0      lazyeval_0.2.0       data.table_1.9.6    
[16] annotate_1.52.0      rpart_4.1-10         Matrix_1.2-6         labeling_0.3         splines_3.3.1       
[21] BiocParallel_1.8.1   geneplotter_1.52.0   stringr_1.1.0        foreign_0.8-66       RCurl_1.95-4.8      
[26] munsell_0.4.3        httpuv_1.3.3         htmltools_0.3.5      nnet_7.3-12          tibble_1.2          
[31] gridExtra_2.2.1      htmlTable_1.7        Hmisc_4.0-0          XML_3.98-1.4         bitops_1.0-6        
[36] grid_3.3.1           jsonlite_1.1         xtable_1.8-2         gtable_0.2.0         DBI_0.5-1           
[41] magrittr_1.5         scales_0.4.0         stringi_1.1.2        XVector_0.14.0       reshape2_1.4.2      
[46] genefilter_1.56.0    latticeExtra_0.6-28  Formula_1.2-1        rjson_0.2.15         RColorBrewer_1.1-2  
[51] tools_3.3.1          survival_2.40-1      AnnotationDbi_1.36.0 colorspace_1.2-7     rhdf5_2.18.0        
[56] cluster_2.0.4        knitr_1.14          

If anyone has any advice as to how I can fix my code, please let me know.

Thanks in advance!

~Lina

Can you run traceback() after the error and report the output?