Question: txtimportData installation on R version 3.3.0 (2016-05-03)
1
gravatar for jarod_v6@libero.it
3.2 years ago by
Italy
jarod_v6@libero.it40 wrote:

Hi there! I need to use tximport.

I have some poblems on intallation of this package:

 

 

https://bioconductor.org/install/#troubleshoot-biocinstaller
> biocLite("tximportData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘tximportData’
Warning message:
package ‘tximportData’ is not available (for R version 3.3.0)

I was able to install tximport but miss some commands..

 

rm(list=ls())

suppressMessages(library( "DESeq" ))
suppressMessages(library("tximport"))

setwd("~/Desktop/Prova_strand")
dir<-"~/Desktop/Prova_strand/"
metadata<-read.table("tipo.csv",header=F)
files=file.path(dir,metadata$V1)
txi.rsem<-tximport(files,type="rsem",reader=read.delim)

sample<-data.frame(condition=factor(c("A","B")))


dds<-DESeqDataSetTxiport(txi.rsem,sample,~1)
Error: could not find function "DESeqDataSetTxiport"

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] edgeR_3.12.1               limma_3.26.9               tximport_1.1.3            
 [4] DESeq2_1.10.1              RcppArmadillo_0.7.100.3.1  Rcpp_0.12.5               
 [7] SummarizedExperiment_1.0.2 Biobase_2.30.0             GenomicRanges_1.22.4      
[10] GenomeInfoDb_1.6.3         IRanges_2.4.8              S4Vectors_0.8.11          
[13] BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.4           XVector_0.10.0      
 [5] futile.options_1.0.0 tools_3.3.0          zlibbioc_1.16.0      rpart_4.1-10        
 [9] RSQLite_1.0.0        annotate_1.48.0      gtable_0.2.0         lattice_0.20-33     
[13] Matrix_1.2-6         DBI_0.4-1            gridExtra_2.2.1      genefilter_1.52.1   
[17] cluster_2.0.4        locfit_1.5-9.1       grid_3.3.0           nnet_7.3-12         
[21] data.table_1.9.6     AnnotationDbi_1.32.3 XML_3.98-1.4         survival_2.39-5     
[25] BiocParallel_1.4.3   foreign_0.8-66       latticeExtra_0.6-28  Formula_1.2-1       
[29] geneplotter_1.48.0   ggplot2_2.1.0        lambda.r_1.1.7       Hmisc_3.17-4        
[33] scales_0.4.0         splines_3.3.0        xtable_1.8-2         colorspace_1.2-6    
[37] acepack_1.3-3.3      munsell_0.4.3        chron_2.3-47

 

 

Someone could please help me?

deseq2 tximport • 2.0k views
ADD COMMENTlink modified 3.1 years ago • written 3.2 years ago by jarod_v6@libero.it40
Answer: txtimportData installation on R version 3.3.0 (2016-05-03)
1
gravatar for jarod_v6@libero.it
3.1 years ago by
Italy
jarod_v6@libero.it40 wrote:

I have installed the new bioconductor version however i have this error:

 

dds<-DESeqDataSetFromTximport(txi.rsem,sample,~1)
using counts and average transcript lengths from tximport
Error: all(lengths > 0) is not TRUE

 head(txi.rsem$counts)
                [,1]   [,2] [,3]
ENSG00000000003    0 160.00    0
ENSG00000000005    2  15.00    2
ENSG00000000419    2  70.00    1
ENSG00000000457   53 246.06   18
ENSG00000000460   54  64.94   24
ENSG00000000938    0   8.00    1

 

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DESeq2_1.12.3                           SummarizedExperiment_1.2.3             
 [3] tximport_1.0.3                          TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [5] GenomicFeatures_1.24.3                  AnnotationDbi_1.34.3                   
 [7] Biobase_2.32.0                          GenomicRanges_1.24.2                   
 [9] GenomeInfoDb_1.8.1                      IRanges_2.6.1                          
[11] S4Vectors_0.10.1                        BiocGenerics_0.18.0                    
[13] tximportData_1.0.2                      knitr_1.13                             

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5             RColorBrewer_1.1-2      plyr_1.8.4             
 [4] XVector_0.12.0          bitops_1.0-6            tools_3.3.1            
 [7] zlibbioc_1.18.0         rpart_4.1-10            biomaRt_2.28.0         
[10] annotate_1.50.0         RSQLite_1.0.0           gtable_0.2.0           
[13] lattice_0.20-33         Matrix_1.2-6            DBI_0.4-1              
[16] gridExtra_2.2.1         genefilter_1.54.2       cluster_2.0.4          
[19] rtracklayer_1.32.1      Biostrings_2.40.2       locfit_1.5-9.1         
[22] nnet_7.3-12             grid_3.3.1              data.table_1.9.6       
[25] XML_3.98-1.4            survival_2.39-5         BiocParallel_1.6.2     
[28] foreign_0.8-66          latticeExtra_0.6-28     Formula_1.2-1          
[31] geneplotter_1.50.0      ggplot2_2.1.0           Rsamtools_1.24.0       
[34] Hmisc_3.17-4            scales_0.4.0            GenomicAlignments_1.8.3
[37] splines_3.3.1           xtable_1.8-2            colorspace_1.2-6       
[40] acepack_1.3-3.3         RCurl_1.95-4.8          munsell_0.4.3          
[43] chron_2.3-47  
ADD COMMENTlink written 3.1 years ago by jarod_v6@libero.it40
1

hi, 

This error is because the modeling cannot have transcripts of length zero included in the offset calculation. What does it mean to have a gene of length 0 after all?

I don't know the best solution here, the zeros are being produced by the upstream software, but I've recommended to others to just insert a length of 1 instead for these 0's, before moving on to DESeq2:

txi$length[txi$length == 0] <- 1
ADD REPLYlink written 3.1 years ago by Michael Love24k
Answer: txtimportData installation on R version 3.3.0 (2016-05-03)
0
gravatar for Michael Love
3.2 years ago by
Michael Love24k
United States
Michael Love24k wrote:
tximportData is only available for Bioconductor 3.3. It says here you are using version 3.2.
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Michael Love24k
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