Question: can not obtain DESeq2 results
1
1
Entering edit mode
9 months ago
zjxia ▴ 10

Dear all, I am trying to run DESeq2 to get the list of differential expressed genes between tumor and normal samples. However I could not get result:

code:

group=c(rep("normal",39),rep("tumor",81))
condition <- factor(group,levels = c("normal","tumor"))
coldata <- data.frame(row.names=colnames(data), condition)
dds <- DESeqDataSetFromMatrix(countData = data, colData = coldata, design= ~ condition )
dds <- DESeq(dds) 
res <- results(dds, contrast=c("condition","normal","tumor"))

error info:
> resultsNames(dds)

[1] "Intercept"                 "condition_tumor_vs_normal"

> res <- results(dds, name ="condition_tumor_vs_normal")

Error in .wrap_in_length_one_list_like_object(value, name, x) : failed to coerce 'list(value)' to a DESeqResults object of length 1

> res <- results(dds, contrast=c("condition","normal","tumor"))

Error in .wrap_in_length_one_list_like_object(value, name, x) : failed to coerce 'list(value)' to a DESeqResults object of length 1

I don't know mistakes in my code and I would appreciate any suggestions.

Zongjun

DESeq2 RNA-Seq Forum • 563 views
ADD COMMENT
0
Entering edit mode

Did you try googling? Put up your sessionInfo.

ADD REPLY
0
Entering edit mode

yes, but found no tips

ADD REPLY
0
Entering edit mode
ADD REPLY
0
Entering edit mode

I uninstalled 14 too new package, and reinstalled "DESeq2" and dependent package use BiocManager::install, error remains unsolved.

> res <- results(dds, contrast=c("condition","normal","tumor"))

Error in .wrap_in_length_one_list_like_object(value, name, x) : 
  failed to coerce 'list(value)' to a DESeqResults object of length 1

> BiocManager::valid()
[1] TRUE

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8

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

other attached packages:
 [1] DESeq2_1.24.0               lattice_0.20-41             locfit_1.5-9.4             
 [4] limma_3.40.6                SummarizedExperiment_1.14.1 DelayedArray_0.10.0        
 [7] BiocParallel_1.18.1         matrixStats_0.56.0          Biobase_2.44.0             
[10] GenomicRanges_1.36.1        GenomeInfoDb_1.20.0         IRanges_2.18.3             
[13] S4Vectors_0.22.1            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] bit64_0.9-7            splines_3.6.3          Formula_1.2-3          BiocManager_1.30.10   
 [5] latticeExtra_0.6-29    blob_1.2.1             GenomeInfoDbData_1.2.1 pillar_1.4.6          
 [9] RSQLite_2.2.0          backports_1.1.8        glue_1.4.1             digest_0.6.25         
[13] RColorBrewer_1.1-2     XVector_0.24.0         checkmate_2.0.0        colorspace_1.4-1      
[17] htmltools_0.5.0        Matrix_1.2-18          XML_3.99-0.3           pkgconfig_2.0.3       
[21] genefilter_1.66.0      zlibbioc_1.30.0        purrr_0.3.4            xtable_1.8-4          
[25] scales_1.1.1           jpeg_0.1-8.1           htmlTable_2.0.1        tibble_3.0.3          
[29] annotate_1.62.0        generics_0.0.2         ggplot2_3.3.2          ellipsis_0.3.1        
[33] nnet_7.3-14            survival_3.2-3         magrittr_1.5           crayon_1.3.4          
[37] memoise_1.1.0          foreign_0.8-75         tools_3.6.3            data.table_1.12.8     
[41] lifecycle_0.2.0        stringr_1.4.0          munsell_0.5.0          cluster_2.1.0         
[45] AnnotationDbi_1.46.1   compiler_3.6.3         rlang_0.4.7            grid_3.6.3            
[49] RCurl_1.98-1.2         rstudioapi_0.11        htmlwidgets_1.5.1      bitops_1.0-6          
[53] base64enc_0.1-3        gtable_0.3.0           DBI_1.1.0              R6_2.4.1              
[57] gridExtra_2.3          knitr_1.29             dplyr_1.0.0            bit_1.1-15.2          
[61] Hmisc_4.4-0            stringi_1.4.6          Rcpp_1.0.5             geneplotter_1.62.0    
[65] vctrs_0.3.1            rpart_4.1-15           acepack_1.4.1          png_0.1-7             
[69] tidyselect_1.1.0       xfun_0.15
ADD REPLY
0
Entering edit mode
9 months ago
zjxia ▴ 10

Thanks everyone, I have resolved the problem. Upgrade the Bioconductor(3.9->3.10), and together 50 packages were updated. The version of DESeq2 was upgrade from 1.24 to 1.26, then the error disappeared.

ADD COMMENT

Login before adding your answer.

Traffic: 2391 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6