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Description
When I run the Minfi, I got error message cannot load annotation package IlluminaHumanMethylationMSAanno.20a1.hg38
please look at the following :
library(minfi)
library(IlluminaHumanMethylationMSAmanifest)
rawSet = read.metharray.exp(base=idatPath, targets=samp, force=TRUE, verbose=T)
rawSet@annotation <- c(array = "IlluminaHumanMethylationMSA", annotation = "20a1.hg38")
rawSet
class: RGChannelSet
dim: 384497 48
metadata(0):
assays(2): Green Red
rownames(384497): 1600237 1600273 ... 99810982 99810988
rowData names(0):
colnames(48): 209291580033_R01C01 209291580033_R02C01 ...
209291580033_R15C03 209291580033_R16C03
colData names(41): Index SampleID ... Sample_Name filenames
Annotation
array: IlluminaHumanMethylationMSA
annotation: 20a1.hg38
RGset.raw <- preprocessRaw(rawSet)
psex <- getSex(mapToGenome(RGset.raw))
Loading required package: IlluminaHumanMethylationMSAanno.20a1.hg38
Error in getAnnotationObject(object) :
cannot load annotation package IlluminaHumanMethylationMSAanno.20a1.hg38
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘IlluminaHumanMethylationMSAanno.20a1.hg38’
sessionInfo()
R version 4.4.3 (2025-02-28)
Platform: x86_64-suse-linux-gnu
Running under: SUSE Linux Enterprise Server 15 SP4
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so; LAPACK version 3.12.0
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
time zone: America/Chicago
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] IlluminaHumanMethylationMSAmanifest_0.1.0
[2] minfi_1.52.1
[3] bumphunter_1.48.0
[4] locfit_1.5-9.12
[5] iterators_1.0.14
[6] foreach_1.5.2
[7] Biostrings_2.74.1
[8] XVector_0.46.0
[9] SummarizedExperiment_1.36.0
[10] Biobase_2.66.0
How to fix the problem?
Thanks for your help.