Skip to content

IlluminaHumanMethylationMSAmanifest #286

@zwang072005

Description

@zwang072005

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions