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:
txi.express <-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) locale:  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252  LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  DESeq2_1.12.4 SummarizedExperiment_1.2.3  TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2 GenomicFeatures_1.24.5  AnnotationDbi_1.34.4 Biobase_2.32.0  GenomicRanges_1.24.3 GenomeInfoDb_1.8.7  IRanges_2.6.1 S4Vectors_0.10.3  BiocGenerics_0.18.0 tximport_1.0.3 loaded via a namespace (and not attached):  genefilter_1.54.2 locfit_1.5-9.1 splines_3.3.1 lattice_0.20-35  colorspace_1.3-2 htmltools_0.3.6 rtracklayer_1.32.2 base64enc_0.1-3  survival_2.41-3 XML_3.98-1.7 foreign_0.8-68 DBI_0.6-1  BiocParallel_1.6.6 RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0  zlibbioc_1.18.0 Biostrings_2.40.2 munsell_0.4.3 gtable_0.2.0  htmlwidgets_0.8 memoise_1.1.0 latticeExtra_0.6-28 knitr_1.15.1  geneplotter_1.50.0 biomaRt_2.28.0 htmlTable_1.9 Rcpp_0.12.10  xtable_1.8-2 acepack_1.4.1 scales_0.4.1 backports_1.0.5  checkmate_1.8.2 annotate_1.50.1 Hmisc_4.0-3 XVector_0.12.1  Rsamtools_1.24.0 gridExtra_2.2.1 ggplot2_2.2.1 digest_0.6.12  stringi_1.1.5 grid_3.3.1 tools_3.3.1 bitops_1.0-6  magrittr_1.5 RCurl_1.95-4.8 lazyeval_0.2.0 RSQLite_1.1-2  tibble_1.3.0 Formula_1.2-1 cluster_2.0.6 Matrix_1.2-10  data.table_1.10.4 rpart_4.1-11 GenomicAlignments_1.8.4 nnet_7.3-12