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Benoit.Fiset
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30
@benoitfiset-18473
Last seen 4.5 years ago
Hi,
This week was the week to upgrade to Bioconductor version '3.8' (from 3.7) so DESeq2 also got a facelift.
So running SAME exact code with new upgraded DESeq2 now getting warnings when running DESeq()
> dds<-DESeq(ddsHTSeq,parallel = TRUE)
estimating size factors
estimating dispersions
gene-wise dispersion estimates: 6 workers
mean-dispersion relationship
final dispersion estimates, fitting model and testing: 6 workers
-- replacing outliers and refitting for 456 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
There were 12 warnings (use warnings() to see them)
> summary(warnings())
12 identical warnings:
In serialize(data, node$con, xdr = FALSE) :
'package:stats' may not be available when loading
>
> sessionInfo()
R version 3.5.1 (2018-07-02)
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/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
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_1.18.1
[9] IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] bit64_0.9-7 splines_3.5.1 Formula_1.2-3 assertthat_0.2.0 latticeExtra_0.6-28
[6] blob_1.1.1 GenomeInfoDbData_1.2.0 yaml_2.2.0 pillar_1.3.0 RSQLite_2.1.1
[11] backports_1.1.2 lattice_0.20-38 glue_1.3.0 digest_0.6.18 RColorBrewer_1.1-2
[16] XVector_0.22.0 checkmate_1.8.5 colorspace_1.3-2 htmltools_0.3.6 Matrix_1.2-15
[21] plyr_1.8.4 XML_3.98-1.16 pkgconfig_2.0.2 genefilter_1.64.0 zlibbioc_1.28.0
[26] purrr_0.2.5 xtable_1.8-3 scales_1.0.0 htmlTable_1.12 tibble_1.4.2
[31] annotate_1.60.0 ggplot2_3.1.0 nnet_7.3-12 lazyeval_0.2.1 survival_2.43-1
[36] magrittr_1.5 crayon_1.3.4 memoise_1.1.0 foreign_0.8-71 tools_3.5.1
[41] data.table_1.11.8 stringr_1.3.1 locfit_1.5-9.1 munsell_0.5.0 cluster_2.0.7-1
[46] AnnotationDbi_1.44.0 bindrcpp_0.2.2 compiler_3.5.1 rlang_0.3.0.1 grid_3.5.1
[51] RCurl_1.95-4.11 rstudioapi_0.8 htmlwidgets_1.3 bitops_1.0-6 base64enc_0.1-3
[56] gtable_0.2.0 DBI_1.0.0 R6_2.3.0 gridExtra_2.3 knitr_1.20
[61] dplyr_0.7.8 bit_1.1-14 bindr_0.1.1 Hmisc_4.1-1 stringi_1.2.4
[66] Rcpp_1.0.0 geneplotter_1.60.0 rpart_4.1-13 acepack_1.4.1 tidyselect_0.2.5
So to validate what is going on, downgraded back to Bioconductor version '3.7' and to DESeq 1.20.0
(BiocManager::install(version = '3.7')
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2", version = "3.7")
> sessionInfo()
R version 3.5.1 (2018-07-02)
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/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq2_1.20.0 SummarizedExperiment_1.10.1 DelayedArray_0.6.6 BiocParallel_1.14.2
[5] matrixStats_0.54.0 Biobase_2.40.0 GenomicRanges_1.32.7 GenomeInfoDb_1.16.0
[9] IRanges_2.14.12 S4Vectors_0.18.3 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] bit64_0.9-7 splines_3.5.1 Formula_1.2-3 assertthat_0.2.0 latticeExtra_0.6-28
[6] blob_1.1.1 GenomeInfoDbData_1.1.0 yaml_2.2.0 pillar_1.3.0 RSQLite_2.1.1
[11] backports_1.1.2 lattice_0.20-38 glue_1.3.0 digest_0.6.18 RColorBrewer_1.1-2
[16] XVector_0.20.0 checkmate_1.8.5 colorspace_1.3-2 htmltools_0.3.6 Matrix_1.2-15
[21] plyr_1.8.4 XML_3.98-1.16 pkgconfig_2.0.2 genefilter_1.62.0 zlibbioc_1.26.0
[26] purrr_0.2.5 xtable_1.8-3 scales_1.0.0 htmlTable_1.12 tibble_1.4.2
[31] annotate_1.58.0 ggplot2_3.1.0 nnet_7.3-12 lazyeval_0.2.1 survival_2.43-1
[36] magrittr_1.5 crayon_1.3.4 memoise_1.1.0 foreign_0.8-71 tools_3.5.1
[41] data.table_1.11.8 stringr_1.3.1 locfit_1.5-9.1 munsell_0.5.0 cluster_2.0.7-1
[46] AnnotationDbi_1.42.1 bindrcpp_0.2.2 compiler_3.5.1 rlang_0.3.0.1 grid_3.5.1
[51] RCurl_1.95-4.11 rstudioapi_0.8 htmlwidgets_1.3 bitops_1.0-6 base64enc_0.1-3
[56] gtable_0.2.0 DBI_1.0.0 R6_2.3.0 gridExtra_2.3 knitr_1.20
[61] dplyr_0.7.8 bit_1.1-14 bindr_0.1.1 Hmisc_4.1-1 stringi_1.2.4
[66] Rcpp_1.0.0 geneplotter_1.58.0 rpart_4.1-13 acepack_1.4.1 tidyselect_0.2.5
dds<-DESeq(ddsHTSeq,parallel = TRUE)
estimating size factors
estimating dispersions
gene-wise dispersion estimates: 6 workers
mean-dispersion relationship
final dispersion estimates, fitting model and testing: 6 workers
-- replacing outliers and refitting for 456 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
>
Now more Warnings... all gone with DESeq2_1.20.0.
And idea what happened between DESeq2_1.20.0 and DESeq2_1.22.1 for these warnings, and how to fix ?
Thanks,
B.
Forgot to write that results(), now with DESeq2_1.22.1, also give the same warning...
> res<-results(dds,parallel = TRUE,contrast=c("condition",sampleLevels)) Warning messages: 1: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 2: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 3: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 4: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 5: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loading 6: In serialize(data, node$con, xdr = FALSE) : 'package:stats' may not be available when loadingIs this with RStudio, or from the command line? If from RStudio, is the same observed from the command line?