Question: Getting an error trying to do tximportData tutorial
gravatar for mogasawara
5 months ago by
mogasawara0 wrote:


I am working through the "Analyzing RNA-seq data with DESeq2"  and have installed the 'tximportData' package. I am getting an error when I am setting the Factor; I've tried factor(), relevel() each individually and also both (which I'm assuming we wouldn't need to) but came across the same error whichever way. Would appreciate any help, thank you.


dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
samples$condition <- factor(rep(c("A","B"),each=3))
rownames(samples) <- samples$run

files <- file.path(dir,"salmon", samples$run, "quant.sf.gz")
names(files) <- samples$run
tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv"))

txi <- tximport(files, type="salmon", tx2gene=tx2gene)
ddsTxi <- DESeqDataSetFromTximport(txi,
                                   colData = samples,
                                   design = ~ condition)
keep <-rowSums(counts(ddsTxi))>=10

ddsTxi$condition <- factor(ddsTxi$condition, levels = c("untreated","treated"))




3: stop("full model matrix is less than full rank")
2: designAndArgChecker(object, betaPrior)
1: DESeq(ddsTxi)

Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DESeq2_1.22.1               SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.0        
 [5] matrixStats_0.54.0          Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.0        
 [9] IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0         tximport_1.10.0            
[13] readr_1.1.1                 tximportData_1.10.0        

loaded via a namespace (and not attached):
 [1] bit64_0.9-7            jsonlite_1.5           splines_3.5.0          Formula_1.2-3          assertthat_0.2.0      
 [6] latticeExtra_0.6-28    blob_1.1.1             GenomeInfoDbData_1.2.0 yaml_2.2.0             RSQLite_2.1.1         
[11] pillar_1.3.0           backports_1.1.2        lattice_0.20-35        glue_1.3.0             digest_0.6.18         
[16] RColorBrewer_1.1-2     XVector_0.22.0         checkmate_1.8.5        colorspace_1.3-2       htmltools_0.3.6       
[21] Matrix_1.2-14          plyr_1.8.4             XML_3.98-1.16          pkgconfig_2.0.2        genefilter_1.64.0     
[26] zlibbioc_1.28.0        purrr_0.2.5            xtable_1.8-3           scales_1.0.0           htmlTable_1.12        
[31] tibble_1.4.2           annotate_1.60.0        ggplot2_3.1.0          nnet_7.3-12            lazyeval_0.2.1        
[36] survival_2.42-6        magrittr_1.5           crayon_1.3.4           memoise_1.1.0          foreign_0.8-70        
[41] tools_3.5.0            data.table_1.11.8      hms_0.4.2              stringr_1.3.1          locfit_1.5-9.1        
[46] munsell_0.5.0          cluster_2.0.7-1        AnnotationDbi_1.44.0   bindrcpp_0.2.2         compiler_3.5.0        
[51] rlang_0.3.0.1          grid_3.5.0             RCurl_1.95-4.11        rstudioapi_0.8         htmlwidgets_1.3       
[56] bitops_1.0-6           base64enc_0.1-3        gtable_0.2.0           DBI_1.0.0              R6_2.3.0              
[61] gridExtra_2.3          knitr_1.20             dplyr_0.7.7            bit_1.1-14             bindr_0.1.1           
[66] Hmisc_4.1-1            stringi_1.2.4          Rcpp_1.0.0             geneplotter_1.60.0     rpart_4.1-13          
[71] acepack_1.4.1          tidyselect_0.2.5      

deseq2 tximport • 191 views
ADD COMMENTlink modified 5 months ago by Michael Love23k • written 5 months ago by mogasawara0
Answer: Getting an error trying to do tximportData tutorial
gravatar for Michael Love
5 months ago by
Michael Love23k
United States
Michael Love23k wrote:

This step is the one generating the error:

ddsTxi$condition <- factor(ddsTxi$condition, levels = c("untreated","treated"))

If you take a look at ddsTxi$condition after you do this, you've made NAs. If you want to change the names of the levels, you shouldn't do this:

> x <- factor(c("A","B"))
> factor(x, levels=c("C","D"))
[1] <NA> <NA>
Levels: C D

Instead you should do:

> levels(x) <- c("C","D")
> x
[1] C D
Levels: C D



ADD COMMENTlink written 5 months ago by Michael Love23k

Oh, I see, thank you very much. Yes, I did observe that NAs but I didn't understand that was the cause of my error. I was assuming that with the factor(), we could change the names. I was looking at the Conditions column that had "A" and "B" and so I thought for some reason it would change to "untreated" and "treated" as that's what was labeled in the results output. It also showed in my output that the names *didn't* change when I tried it, but I thought I was missing something. I appreciate your quick response! 

ADD REPLYlink written 5 months ago by mogasawara0
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