error with sesameQC on Mouse MM285 Array

[oheil]

I get the following error with Mouse Methylation arrays:

Error in x[...] <- m : NAs are not allowed in subscripted assignments

Can be reproduced with:

library("sesame") 
res_grn = sesameDataDownload("204637490002_R05C01_Grn.idat")
res_red = sesameDataDownload("204637490002_R05C01_Red.idat")
pfx = sprintf("%s/204637490002_R05C01", res_red$dest_dir)
sdf = readIDATpair(pfx)
sesameQC(sdf)

R-4.1.2

Is this known and is there something I can do to avoid this?

[zwdzwd]

Could you show me your sessionInfo? I am not getting this with R4.1.0.

Btw, the devel now has switched to a different interface for QC, which is more flexible hopefully.
https://bioconductor.org/packages/devel/bioc/vignettes/sesame/inst/doc/QC.html

[oheil]

Thanks for the fast response:

> library("sesame")
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS:   /home/worker/R-4.1.2/lib/R/lib/libRblas.so
LAPACK: /home/worker/R-4.1.2/lib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] sesame_1.12.7       sesameData_1.12.0   rmarkdown_2.11
[4] ExperimentHub_2.2.1 AnnotationHub_3.2.1 BiocFileCache_2.2.1
[7] dbplyr_2.1.1        BiocGenerics_0.40.0

loaded via a namespace (and not attached):
[1] bitops_1.0-7                  matrixStats_0.61.0
[3] bit64_4.0.5                   filelock_1.0.2
[5] RColorBrewer_1.1-2            httr_1.4.2
[7] GenomeInfoDb_1.30.0           tools_4.1.2
[9] utf8_1.2.2                    R6_2.5.1
[11] KernSmooth_2.23-20            DBI_1.1.2
[13] colorspace_2.0-2              DNAcopy_1.68.0
[15] tidyselect_1.1.1              gridExtra_2.3
[17] preprocessCore_1.56.0         bit_4.0.4
[19] curl_4.3.2                    compiler_4.1.2
[21] cli_3.1.1                     Biobase_2.54.0
[23] DelayedArray_0.20.0           scales_1.1.1
[25] randomForest_4.6-14           proxy_0.4-26
[27] rappdirs_0.3.3                stringr_1.4.0
[29] digest_0.6.29                 XVector_0.34.0
[31] pkgconfig_2.0.3               htmltools_0.5.2
[33] MatrixGenerics_1.6.0          fastmap_1.1.0
[35] rlang_1.0.0                   RSQLite_2.2.9
[37] shiny_1.7.1                   generics_0.1.1
[39] wheatmap_0.1.0                BiocParallel_1.28.3
[41] dplyr_1.0.7                   RCurl_1.98-1.5
[43] magrittr_2.0.2                GenomeInfoDbData_1.2.7
[45] Matrix_1.4-0                  Rcpp_1.0.8
[47] munsell_0.5.0                 S4Vectors_0.32.3
[49] fansi_1.0.2                   lifecycle_1.0.1
[51] stringi_1.7.6                 yaml_2.2.2
[53] SummarizedExperiment_1.24.0   zlibbioc_1.40.0
[55] plyr_1.8.6                    grid_4.1.2
[57] blob_1.2.2                    parallel_4.1.2
[59] promises_1.2.0.1              ggrepel_0.9.1
[61] crayon_1.4.2                  lattice_0.20-45
[63] Biostrings_2.62.0             KEGGREST_1.34.0
[65] knitr_1.37                    pillar_1.6.5
[67] GenomicRanges_1.46.1          fgsea_1.20.0
[69] reshape2_1.4.4                stats4_4.1.2
[71] fastmatch_1.1-3               glue_1.6.1
[73] BiocVersion_3.14.0            evaluate_0.14
[75] data.table_1.14.2             BiocManager_1.30.16
[77] png_0.1-7                     vctrs_0.3.8
[79] httpuv_1.6.5                  gtable_0.3.0
[81] purrr_0.3.4                   assertthat_0.2.1
[83] cachem_1.0.6                  ggplot2_3.3.5
[85] xfun_0.29                     mime_0.12
[87] xtable_1.8-4                  e1071_1.7-9
[89] later_1.3.0                   class_7.3-20
[91] tibble_3.1.6                  AnnotationDbi_1.56.2
[93] memoise_2.0.1                 IRanges_2.28.0
[95] ellipsis_0.3.2                interactiveDisplayBase_1.32.0

[zwdzwd]

Looks like it's a channel inference bug (already fixed in devel but I forgot to fix in 1.12). Could you try the new 1.12.8? just uploaded to github but need a few days to get on BioC. Thanks for reporting!

[oheil]

I wasn't able to build it for now. Downloaded RELEASE_3_14 tag (right?) but I get

pandoc: Could not determine mime type for `/home/worker/R-4.1.2/lib/R/library/rmarkdown/rmd/h/fontawesome/css/../webfonts/fa-brands-400.woff2'

I guess that debian jessie is too old for a recent pandoc version with support for woff2.
Giving up here for now and waiting for the update of the bioconductor version.

[oheil]

I have upgraded to version 1.12.8 and it seems to be fine now.
Many thanks !