Error encounter during EPIC methylation analysis

[sarah91-RA]

Hi Everyone,

I am currently experiencing an error while performing EPIC methylation analysis. This has not happened before and recently I encountered this error which happened when I was trying to perform "detectionP " on methyl channels. The error is as follow;

Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE

I am sharing the commands and packages

library(limma)
library(minfi)
library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
library(IlluminaHumanMethylationEPICmanifest)
library(missMethyl)
library(minfiData)
library(RColorBrewer)
library(Gviz)
library(DMRcate)
library(stringr)

Commands are ;
Epic850k= getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
head(Epic850k)

targets <- read.metharray.sheet(dataDirectory, pattern="ILMLEPIC-16516_SampleSheet_updated150124.csv")
targets

rgSet <-read.metharray.exp(targets=targets)
rgSet

pData(rgSet)
getManifest(rgSet)

targets$ID <- paste(targets$Sample_Group,targets$Sample_Name,sep=".")

sampleNames(rgSet) <- targets$ID
rgSet

calculate the detection P-values

>0.01 p-value indicatepoor samples

detP<- detectionP(rgSet)

After applying the detection command, I got the error that I mentioned above. If anyone knows how to resolve this issue please let me know.

[yhoogstrate]

I think this has now become a really urgent issue.

(delayed)matrixstats up to recently was giving the following warnings when running detP:

> detP <- detectionP(rgSet)
Warning messages:
1: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.
2: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.
3: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.
4: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.

However, as of the latest version (matrixStats 1.2.*), the deprecation warning has become a fatal error and detectionP cannot be performed anymore.

I am not sure where/how this relates to the entire dependency structure, so I do not have the capabilities to resolve it myself. Is there anyone who can look into this?

kind regards,

Youri

[kasperdanielhansen]

I cannot replicate this error with a recent install of minfi. Could you please report both

1. the output of sessionInfo()
2. the output of

library(BiocManager)
BiocManager::valid()

[kasperdanielhansen]

I am guessing this may be related to you mixing an older version of minfi with a newer version of matrixStats

[yhoogstrate]

Dear Kasper,

Thank you for the quick response. We're running on a system that is running for 2 years, probably with some R packages installed through Red Hat. The issue appeared on a brand new user with brand new home directory after his first time installing minfi (BiocManager::install("minfi")), yesterday or the day before.

Here is the output of your requested commands (please note that matrixStats is new back to 1.1.0, I copied it from another user as work-around for the issue):

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)
 
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so
 
locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      


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

other attached packages:
[1] readxl_1.4.3                                        dplyr_1.1.4                                       
 [3] stringr_1.5.1                                       minfiData_0.44.0                                  
 [5] IlluminaHumanMethylation450kmanifest_0.4.0          missMethyl_1.32.1                                 
 [7] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1  RColorBrewer_1.1-3                                
 [9] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 limma_3.54.2                                       
[11] knitr_1.46                                          IlluminaHumanMethylationEPICmanifest_0.3.0        
[13] minfi_1.44.0                                        bumphunter_1.40.0                                 
[15] locfit_1.5-9.9                                      iterators_1.0.14                                  
[17] foreach_1.5.2                                       Biostrings_2.66.0                                 
[19] XVector_0.38.0                                      SummarizedExperiment_1.28.0                       
[21] Biobase_2.58.0                                      MatrixGenerics_1.10.0                             
[23] GenomicRanges_1.50.2                                GenomeInfoDb_1.34.9                                
[25] IRanges_2.32.0                                      S4Vectors_0.36.2                                  
[27] BiocGenerics_0.44.0                                 matrixStats_1.1.0                                 
 
loaded via a namespace (and not attached):
  [1] rjson_0.2.21              siggenes_1.72.0           mclust_6.1                base64_2.0.1            
  [5] bit64_4.0.5               AnnotationDbi_1.60.2      fansi_1.0.6               xml2_1.3.6               
  [9] codetools_0.2-20          splines_4.2.2             sparseMatrixStats_1.10.0  cachem_1.0.8            
 [13] scrime_1.3.5              Rsamtools_2.14.0          annotate_1.76.0           dbplyr_2.5.0            
 [17] png_0.1-8                 HDF5Array_1.26.0          BiocManager_1.30.22       readr_2.1.5             
 [21] compiler_4.2.2            httr_1.4.7                Matrix_1.6-5              fastmap_1.1.1           
 [25] cli_3.6.2                 prettyunits_1.2.0         tools_4.2.2               glue_1.7.0              
 [29] GenomeInfoDbData_1.2.9    rappdirs_0.3.3            doRNG_1.8.6               Rcpp_1.0.12             
 [33] cellranger_1.1.0          vctrs_0.6.5               rhdf5filters_1.10.1       multtest_2.54.0          
 [37] preprocessCore_1.60.2     nlme_3.1-164              rtracklayer_1.58.0        DelayedMatrixStats_1.20.0
[41] xfun_0.43                 lifecycle_1.0.4           restfulr_0.0.15           rngtools_1.5.2          
 [45] statmod_1.5.0             XML_3.99-0.16.1           beanplot_1.3.1            org.Hs.eg.db_3.16.0     
 [49] zlibbioc_1.44.0           MASS_7.3-60.0.1           hms_1.1.3                 rhdf5_2.42.1            
 [53] GEOquery_2.66.0           yaml_2.3.8                curl_5.2.1                memoise_2.0.1           
 [57] biomaRt_2.54.1            reshape_0.8.9             stringi_1.8.3             RSQLite_2.3.6           
 [61] genefilter_1.80.3         BiocIO_1.8.0              GenomicFeatures_1.50.4    filelock_1.0.3           
 [65] BiocParallel_1.32.6       rlang_1.1.3               pkgconfig_2.0.3           bitops_1.0-7            
 [69] nor1mix_1.3-3             lattice_0.22-6            purrr_1.0.2               Rhdf5lib_1.20.0         
 [73] GenomicAlignments_1.34.1  bit_4.0.5                 tidyselect_1.2.1          plyr_1.8.9              
 [77] magrittr_2.0.3            R6_2.5.1                  generics_0.1.3            DelayedArray_0.24.0     
 [81] DBI_1.2.2                 withr_3.0.0               pillar_1.9.0              survival_3.6-4          
 [85] KEGGREST_1.38.0           RCurl_1.98-1.14           tibble_3.2.1              crayon_1.5.2            
 [89] utf8_1.2.4                BiocFileCache_2.6.1       tzdb_0.4.0                progress_1.2.3          
 [93] grid_4.2.2                data.table_1.15.4         blob_1.2.4                digest_0.6.35           
 [97] xtable_1.8-4              tidyr_1.3.1               illuminaio_0.40.0         openssl_2.1.2           
[101] askpass_1.2.0             quadprog_1.5-8

> library(BiocManager)
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31)
Bioconductor version '3.16' is out-of-date; the current release version '3.18' is available with R version '4.3'; see
  https://bioconductor.org/install
> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for
details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
 
* sessionInfo()
 
R version 4.2.2 (2022-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)
 
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so
 
locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      
 
attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base    
 
other attached packages:
[1] BiocManager_1.30.22                                 readxl_1.4.3                                      
 [3] dplyr_1.1.4                                         stringr_1.5.1                                     
 [5] minfiData_0.44.0                                    IlluminaHumanMethylation450kmanifest_0.4.0        
 [7] missMethyl_1.32.1                                   IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
 [9] RColorBrewer_1.1-3                                  IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[11] limma_3.54.2                                        knitr_1.46                                         
[13] IlluminaHumanMethylationEPICmanifest_0.3.0          minfi_1.44.0                                      
[15] bumphunter_1.40.0                                   locfit_1.5-9.9                                    
[17] iterators_1.0.14                                    foreach_1.5.2                                     
[19] Biostrings_2.66.0                                   XVector_0.38.0                                    
[21] SummarizedExperiment_1.28.0                         Biobase_2.58.0                                    
[23] MatrixGenerics_1.10.0                               GenomicRanges_1.50.2                              
[25] GenomeInfoDb_1.34.9                                 IRanges_2.32.0                                     
[27] S4Vectors_0.36.2                                    BiocGenerics_0.44.0                               
[29] matrixStats_1.1.0                                 
 
loaded via a namespace (and not attached):
  [1] rjson_0.2.21              siggenes_1.72.0           mclust_6.1                base64_2.0.1            
  [5] bit64_4.0.5               AnnotationDbi_1.60.2      fansi_1.0.6               xml2_1.3.6              
  [9] codetools_0.2-20          splines_4.2.2             sparseMatrixStats_1.10.0  cachem_1.0.8            
 [13] scrime_1.3.5              Rsamtools_2.14.0          annotate_1.76.0           dbplyr_2.5.0            
 [17] png_0.1-8                 HDF5Array_1.26.0          readr_2.1.5               compiler_4.2.2          
 [21] httr_1.4.7                Matrix_1.6-5              fastmap_1.1.1             cli_3.6.2               
 [25] prettyunits_1.2.0         tools_4.2.2               glue_1.7.0                GenomeInfoDbData_1.2.9  
 [29] rappdirs_0.3.3            doRNG_1.8.6               Rcpp_1.0.12               cellranger_1.1.0        
 [33] vctrs_0.6.5               rhdf5filters_1.10.1       multtest_2.54.0           preprocessCore_1.60.2   
 [37] nlme_3.1-164              rtracklayer_1.58.0        DelayedMatrixStats_1.20.0 xfun_0.43               
 [41] lifecycle_1.0.4           restfulr_0.0.15           rngtools_1.5.2            statmod_1.5.0           
 [45] XML_3.99-0.16.1           beanplot_1.3.1            org.Hs.eg.db_3.16.0       zlibbioc_1.44.0         
 [49] MASS_7.3-60.0.1           hms_1.1.3                 rhdf5_2.42.1              GEOquery_2.66.0         
 [53] yaml_2.3.8                curl_5.2.1                memoise_2.0.1             biomaRt_2.54.1          
 [57] reshape_0.8.9             stringi_1.8.3             RSQLite_2.3.6             genefilter_1.80.3       
 [61] BiocIO_1.8.0              GenomicFeatures_1.50.4    filelock_1.0.3            BiocParallel_1.32.6     
 [65] rlang_1.1.3               pkgconfig_2.0.3           bitops_1.0-7              nor1mix_1.3-3           
 [69] lattice_0.22-6            purrr_1.0.2               Rhdf5lib_1.20.0           GenomicAlignments_1.34.1
 [73] bit_4.0.5                 tidyselect_1.2.1          plyr_1.8.9                magrittr_2.0.3          
 [77] R6_2.5.1                  generics_0.1.3            DelayedArray_0.24.0       DBI_1.2.2               
 [81] withr_3.0.0               pillar_1.9.0              survival_3.6-4            KEGGREST_1.38.0          
 [85] RCurl_1.98-1.14           tibble_3.2.1              crayon_1.5.2              utf8_1.2.4              
 [89] BiocFileCache_2.6.1       tzdb_0.4.0                progress_1.2.3            grid_4.2.2              
 [93] data.table_1.15.4         blob_1.2.4                digest_0.6.35             xtable_1.8-4            
 [97] tidyr_1.3.1               illuminaio_0.40.0         openssl_2.1.2             askpass_1.2.0           
[101] quadprog_1.5-8          
 
Bioconductor version '3.16'
 
  * 2 packages out-of-date
  * 0 packages too new
 
create a valid installation with
 
  BiocManager::install(c(
    "matrixStats", "mclust"
  ), update = TRUE, ask = FALSE, force = TRUE)
 
more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
 
Warning message:
2 packages out-of-date; 0 packages too new

If we need to do any testing or can be of help in any other way, feel free to ask.

Youri