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Question: results function of DESeq2 devel fails
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gravatar for matthias.zytnicki
8 months ago by
matthias.zytnicki0 wrote:

I tried to follow the DESeq2 tutorial, and ended up with a error.

library("pasilla")
library("DESeq2")
pasCts <- system.file("extdata", "pasilla_gene_counts.tsv", package="pasilla", mustWork=TRUE)
pasAnno <- system.file("extdata", "pasilla_sample_annotation.csv", package="pasilla", mustWork=TRUE)
cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
coldata <- read.csv(pasAnno, row.names=1)
coldata <- coldata[,c("condition","type")]
rownames(coldata) <- sub("fb", "", rownames(coldata))
cts <- cts[, rownames(coldata)]
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
featureData <- data.frame(gene=rownames(cts))
mcols(dds) <- DataFrame(mcols(dds), featureData)
dds <- DESeq(dds)
res <- results(dds)

The error is:

Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) :
  the objects to concatenate must be DESeqResults objects (or NULLs)

Should I wait the new version? Is the new version different from the previous ones?

R Under development (unstable) (2018-01-08 r74099)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DESeq2_1.19.14             SummarizedExperiment_1.9.5
 [3] DelayedArray_0.5.15        BiocParallel_1.13.1       
 [5] matrixStats_0.52.2         Biobase_2.39.1            
 [7] GenomicRanges_1.31.3       GenomeInfoDb_1.15.1       
 [9] IRanges_2.13.5             S4Vectors_0.17.17         
[11] BiocGenerics_0.25.1        pasilla_1.7.0             

loaded via a namespace (and not attached):
 [1] genefilter_1.61.0      locfit_1.5-9.1         splines_3.5.0         
 [4] lattice_0.20-35        colorspace_1.3-2       htmltools_0.3.6       
 [7] base64enc_0.1-3        blob_1.1.0             survival_2.41-3       
[10] XML_3.98-1.9           rlang_0.1.6            pillar_1.0.1          
[13] DBI_0.7                foreign_0.8-70         bit64_0.9-7           
[16] RColorBrewer_1.1-2     GenomeInfoDbData_1.1.0 plyr_1.8.4            
[19] stringr_1.2.0          zlibbioc_1.25.0        munsell_0.4.3         
[22] gtable_0.2.0           htmlwidgets_0.9        memoise_1.1.0         
[25] latticeExtra_0.6-28    knitr_1.18             geneplotter_1.57.0    
[28] AnnotationDbi_1.41.4   htmlTable_1.11.1       Rcpp_0.12.14          
[31] acepack_1.4.1          xtable_1.8-2           scales_0.5.0          
[34] backports_1.1.2        checkmate_1.8.5        Hmisc_4.1-1           
[37] annotate_1.57.2        XVector_0.19.1         bit_1.1-12            
[40] gridExtra_2.3          ggplot2_2.2.1          digest_0.6.13         
[43] stringi_1.1.6          grid_3.5.0             tools_3.5.0           
[46] bitops_1.0-6           magrittr_1.5           RSQLite_2.0           
[49] lazyeval_0.2.1         RCurl_1.95-4.10        tibble_1.4.1          
[52] Formula_1.2-2          cluster_2.0.6          Matrix_1.2-12         
[55] data.table_1.10.4-3    rstudioapi_0.7         rpart_4.1-12          
[58] nnet_7.3-12            compiler_3.5.0

BTW: thanks a lot to the DESeq2 team. You are doing a wonderful job.

ADD COMMENTlink written 8 months ago by matthias.zytnicki0

I get this same error for my devel branch packages. I'll look into it today.

ADD REPLYlink written 8 months ago by Michael Love19k

I haven't figured a solution but I have a minimal example. The problem comes when I try to add the padj column to res:

res$padj <- padj

Where res is a DESeqResults object, which contains DataFrame.

I get the same error with this simple example:

setClass("myDataFrame", contains="DataFrame")
d <- DataFrame(x=1:5)
dd <- new("myDataFrame", d)
d$y <- 1:5
dd$y <- 1:5
Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) : 
  the objects to concatenate must be myDataFrame objects (or NULLs)
Calls: $<- ... c -> .local -> concatenateObjects -> concatenateObjects

With this traceback():

> traceback()
19: stop(wmsg("the objects to concatenate must be ", class(.Object), 
        " objects (or NULLs)"))
18: concatenateObjects(x, objects, ignore.mcols = ignore.mcols)
17: concatenateObjects(x, objects, ignore.mcols = ignore.mcols)
16: .local(x, ...)
15: c(x, value)
14: c(x, value)
13: coerce2(c(x, value), x)
12: coerce2(c(x, value), x)
11: .append_list_element(x, value, name)
10: setListElement(x, i, value)
9: setListElement(x, i, value)
8: .nextMethod(x, i, value = value)
7: eval(call, callEnv)
6: eval(call, callEnv)
5: callNextMethod(x, i, value = value)
4: `[[<-`(`*tmp*`, name, value = 1:5)
3: `[[<-`(`*tmp*`, name, value = 1:5)
2: `$<-`(`*tmp*`, y, value = 1:5)
1: `$<-`(`*tmp*`, y, value = 1:5)

> sessionInfo()
R Under development (unstable) (2017-12-07 r73859)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Users/love/bin/R/lib/libRblas.dylib
LAPACK: /Users/love/bin/R/lib/libRlapack.dylib

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 datasets  utils    
[8] methods   base     

other attached packages:
 [1] apeglm_1.1.9               DESeq2_1.19.15            
 [3] airway_0.113.0             SummarizedExperiment_1.9.5
 [5] DelayedArray_0.5.15        BiocParallel_1.13.1       
 [7] matrixStats_0.52.2         Biobase_2.39.1            
 [9] GenomicRanges_1.31.3       GenomeInfoDb_1.15.1       
[11] IRanges_2.13.5             S4Vectors_0.17.17         
[13] BiocGenerics_0.25.1        BiocInstaller_1.29.3      
[15] rmarkdown_1.8              testthat_2.0.0            
[17] devtools_1.13.4           

loaded via a namespace (and not attached):
 [1] bit64_0.9-7            splines_3.5.0          Formula_1.2-2         
 [4] latticeExtra_0.6-28    blob_1.1.0             GenomeInfoDbData_1.1.0
 [7] numDeriv_2016.8-1      pillar_1.0.1           RSQLite_2.0           
[10] backports_1.1.1        lattice_0.20-35        bbmle_1.0.20          
[13] digest_0.6.12          RColorBrewer_1.1-2     XVector_0.19.1        
[16] checkmate_1.8.5        colorspace_1.3-2       htmltools_0.3.6       
[19] Matrix_1.2-12          plyr_1.8.4             XML_3.98-1.9          
[22] emdbook_1.3.9          genefilter_1.61.0      zlibbioc_1.25.0       
[25] xtable_1.8-2           scales_0.5.0           htmlTable_1.11.1      
[28] tibble_1.4.1           annotate_1.57.2        ggplot2_2.2.1         
[31] withr_2.1.1            nnet_7.3-12            lazyeval_0.2.1        
[34] survival_2.41-3        magrittr_1.5           memoise_1.1.0         
[37] evaluate_0.10.1        MASS_7.3-48            xml2_1.1.1            
[40] foreign_0.8-70         tools_3.5.0            data.table_1.10.4-3   
[43] stringr_1.2.0          locfit_1.5-9.1         munsell_0.4.3         
[46] cluster_2.0.6          AnnotationDbi_1.41.4   compiler_3.5.0        
[49] rlang_0.1.6            grid_3.5.0             RCurl_1.95-4.8        
[52] rstudioapi_0.7         htmlwidgets_0.9        bitops_1.0-6          
[55] base64enc_0.1-3        gtable_0.2.0           roxygen2_6.0.1        
[58] DBI_0.7                R6_2.2.2               gridExtra_2.3         
[61] knitr_1.17             bit_1.1-12             commonmark_1.4        
[64] Hmisc_4.0-3            rprojroot_1.2          stringi_1.1.6         
[67] Rcpp_0.12.14           geneplotter_1.57.0     rpart_4.1-12          
[70] acepack_1.4.1          coda_0.19-1     
ADD REPLYlink written 8 months ago by Michael Love19k

I started a new thread here to see if S4Vectors authors can helpĀ 

Adding a column to a class that contains DataFrame

ADD REPLYlink written 8 months ago by Michael Love19k

Thanks a lot!

I will wait for their fix.

(BTW: BioConductor recommends that seq_len() or seq_along() be used instead of 1:... :-)

ADD REPLYlink modified 8 months ago • written 8 months ago by matthias.zytnicki0
0
gravatar for Michael Love
8 months ago by
Michael Love19k
United States
Michael Love19k wrote:

It looks like it no longer gives an error, try updating all Bioc packages.

ADD COMMENTlink written 8 months ago by Michael Love19k
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