Question: tximport using for data generated from other tools
gravatar for saumya.kumar
8 months ago by
saumya.kumar0 wrote:


I want to try using tximport on another tool that I am evaluating, eXpress. For this I converted the quantification files  generated by eXpress programatically into salmon's quant.sf format and then thought to give it a try. I get the following error:

reading in files
1 2 Error: all(txId == raw[[txIdCol]]) is not TRUE

This looks like pointing towards the txID, which I have checked in file 2 and it doesn't appear empty at all. I am using this command: <-tximport(Files,type = "salmon", tx2gene = tx2gene)

The tx2gene file consists of Ensembl transcript ids and gene Ids. I have used this file for Salmon results before and it had worked.

 Is there a way I can do this? tximport seems to be able to read file 1 without any error and its at file 2 it seems to give this error. 



> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] DESeq2_1.12.4                            SummarizedExperiment_1.2.3              
 [3] TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2 GenomicFeatures_1.24.5                  
 [5] AnnotationDbi_1.34.4                     Biobase_2.32.0                          
 [7] GenomicRanges_1.24.3                     GenomeInfoDb_1.8.7                      
 [9] IRanges_2.6.1                            S4Vectors_0.10.3                        
[11] BiocGenerics_0.18.0                      tximport_1.0.3                          

loaded via a namespace (and not attached):
 [1] genefilter_1.54.2       locfit_1.5-9.1          splines_3.3.1           lattice_0.20-35        
 [5] colorspace_1.3-2        htmltools_0.3.6         rtracklayer_1.32.2      base64enc_0.1-3        
 [9] survival_2.41-3         XML_3.98-1.7            foreign_0.8-68          DBI_0.6-1              
[13] BiocParallel_1.6.6      RColorBrewer_1.1-2      plyr_1.8.4              stringr_1.2.0          
[17] zlibbioc_1.18.0         Biostrings_2.40.2       munsell_0.4.3           gtable_0.2.0           
[21] htmlwidgets_0.8         memoise_1.1.0           latticeExtra_0.6-28     knitr_1.15.1           
[25] geneplotter_1.50.0      biomaRt_2.28.0          htmlTable_1.9           Rcpp_0.12.10           
[29] xtable_1.8-2            acepack_1.4.1           scales_0.4.1            backports_1.0.5        
[33] checkmate_1.8.2         annotate_1.50.1         Hmisc_4.0-3             XVector_0.12.1         
[37] Rsamtools_1.24.0        gridExtra_2.2.1         ggplot2_2.2.1           digest_0.6.12          
[41] stringi_1.1.5           grid_3.3.1              tools_3.3.1             bitops_1.0-6           
[45] magrittr_1.5            RCurl_1.95-4.8          lazyeval_0.2.0          RSQLite_1.1-2          
[49] tibble_1.3.0            Formula_1.2-1           cluster_2.0.6           Matrix_1.2-10          
[53] data.table_1.10.4       rpart_4.1-11            GenomicAlignments_1.8.4 nnet_7.3-12            


ADD COMMENTlink modified 8 months ago by Michael Love16k • written 8 months ago by saumya.kumar0
gravatar for Michael Love
8 months ago by
Michael Love16k
United States
Michael Love16k wrote:

tximport needs for all the 'files' to have the transcripts in the same order. The package is designed to import quantifications of multiple samples which were run using the same software against the same transcriptome. You can import individual files separately using tximport, if you want to read in files run with multiple software. We do not support the merging of different quantifications across software though.

ADD COMMENTlink written 8 months ago by Michael Love16k
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