Unable to load data "pasillaGenes" in R because DESeq is not installed?
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0
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kanhasunny • 0
@4f07e997
Last seen 22 months ago

Hello,

I am unable to load data "pasillaGenes" in R. Please see below

> data("pasillaGenes") 
Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘pasillaGenes’
Loading required package: DESeq
Error in .requirePackage(package) : 
  unable to find required package ‘DESeq’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DESeq’

I then proceeded to install DESeq but then the below returned.

> BiocManager::install("DESeq")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'DESeq'
Warning message:
package ‘DESeq’ is not available for this version of R

FYI, I already had DESeq2 installed. Please also kindly see my session info below.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/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 utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.30.0               SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [4] MatrixGenerics_1.2.0        matrixStats_0.57.0          GenomicRanges_1.42.0       
 [7] GenomeInfoDb_1.26.2         IRanges_2.24.1              S4Vectors_0.28.1           
[10] BiocGenerics_0.36.0         pasilla_1.18.0

Thank you so much in advance for any help!

DESeq2 pasillaGenes • 1.1k views
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@mikelove
Last seen 1 day ago
United States

It looks like pasilla may need an update so that pasillaGenes can be loaded without the DESeq package which is deprecated.

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JAcky • 0
@d6b8183e
Last seen 4 weeks ago
Israel

Did you find a solution? I'm having the exact same problem with this same warning

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Entering edit mode
@james-w-macdonald-5106
Last seen 31 minutes ago
United States

Please don't add comments to nearly two-year old posts. Start another one. You can link to this post in your new post if you think it's relevant. Also, you need to provide output from running sessionInfo() so we know what versions you are uisng.

The pasillaGenes object hasn't existed since December 2020, when it was deprecated in lieu of the pasillaDEXSeqDataSet. And it doesn't rely on DESeq in the current version of R/Bioconductor. So you should upgrade.

> library(pasilla)
Loading required package: DEXSeq
<snip>
> data(pasillaDEXSeqDataSet)
> dxd
class: DEXSeqDataSet 
dim: 498 14 
metadata(0):
assays(1): counts
rownames(498): FBgn0000256:E001 FBgn0000256:E002 ... FBgn0261573:E015
  FBgn0261573:E016
rowData names(5): featureID groupID exonBaseMean exonBaseVar
  transcripts
colnames: NULL
colData names(4): sample condition type exon

> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

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

other attached packages:
 [1] pasilla_1.24.0              DEXSeq_1.42.0              
 [3] RColorBrewer_1.1-3          AnnotationDbi_1.58.0       
 [5] DESeq2_1.36.0               SummarizedExperiment_1.26.1
 [7] GenomicRanges_1.48.0        GenomeInfoDb_1.32.3        
 [9] IRanges_2.30.1              S4Vectors_0.34.0           
[11] MatrixGenerics_1.8.1        matrixStats_0.62.0         
[13] Biobase_2.56.0              BiocGenerics_0.42.0        
[15] BiocParallel_1.30.3         BiocManager_1.30.18        

loaded via a namespace (and not attached):
 [1] httr_1.4.4             bit64_4.0.5            splines_4.2.0         
 [4] assertthat_0.2.1       statmod_1.4.37         BiocFileCache_2.4.0   
 [7] blob_1.2.3             Rsamtools_2.12.0       GenomeInfoDbData_1.2.8
[10] progress_1.2.2         pillar_1.8.1           RSQLite_2.2.16        
[13] lattice_0.20-45        glue_1.6.2             digest_0.6.29         
[16] XVector_0.36.0         colorspace_2.0-3       Matrix_1.4-1          
[19] XML_3.99-0.10          pkgconfig_2.0.3        biomaRt_2.52.0        
[22] genefilter_1.78.0      zlibbioc_1.42.0        purrr_0.3.4           
[25] xtable_1.8-4           scales_1.2.1           tibble_3.1.8          
[28] annotate_1.74.0        KEGGREST_1.36.3        generics_0.1.3        
[31] ggplot2_3.3.6          ellipsis_0.3.2         cachem_1.0.6          
[34] cli_3.3.0              survival_3.3-1         magrittr_2.0.3        
[37] crayon_1.5.1           memoise_2.0.1          fansi_1.0.3           
[40] xml2_1.3.3             hwriter_1.3.2.1        tools_4.2.0           
[43] prettyunits_1.1.1      hms_1.1.2              lifecycle_1.0.1       
[46] stringr_1.4.1          munsell_0.5.0          locfit_1.5-9.6        
[49] DelayedArray_0.22.0    Biostrings_2.64.1      compiler_4.2.0        
[52] rlang_1.0.4            grid_4.2.0             RCurl_1.98-1.8        
[55] rappdirs_0.3.3         bitops_1.0-7           gtable_0.3.0          
[58] codetools_0.2-18       curl_4.3.2             DBI_1.1.3             
[61] R6_2.5.1               dplyr_1.0.9            fastmap_1.1.0         
[64] bit_4.0.4              utf8_1.2.2             filelock_1.0.2        
[67] stringi_1.7.8          parallel_4.2.0         Rcpp_1.0.9            
[70] vctrs_0.4.1            geneplotter_1.74.0     png_0.1-7             
[73] dbplyr_2.2.1           tidyselect_1.1.2

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