Entering edit mode
Hello,
I am attempting to perform gene enrichment analysis on methylation data. The program can not find the EPIC annotation file. To be sure it was there I downloaded this file using the below command. Following this I received the same error. Could anyone help with this?
if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b2.hg19", version = "3.8")
My code:
myGSEAexp <- champ.GSEA(beta=myNorm, DMP=myDMP[[1]], DMR=DMREX, arraytype="EPIC",adjPval=0.05, method="gometh")
[===========================]
[<<<< ChAMP.GSEA START >>>>>]
-----------------------------
<< Prepare CpG List Ready >>
Calculating GSEA with gometh method on DMP CpG list
Note that gometh method would count numbers of CpGs in each genes and correct this bias.
Error in getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) :
object 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19' not found
>
Session info
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[3] bindrcpp_0.2.2
[4] shiny_1.2.0
[5] ChAMP_2.12.2
[6] IlluminaHumanMethylationEPICmanifest_0.3.0
[7] Illumina450ProbeVariants.db_1.18.0
[8] DMRcate_1.18.0
[9] DMRcatedata_1.18.0
[10] DSS_2.30.1
[11] bsseq_1.18.0
[12] FEM_3.10.0
[13] graph_1.60.0
[14] org.Hs.eg.db_3.7.0
[15] impute_1.56.0
[16] igraph_1.2.2
[17] corrplot_0.84
[18] marray_1.60.0
[19] limma_3.38.3
[20] Matrix_1.2-14
[21] AnnotationDbi_1.44.0
[22] ChAMPdata_2.14.0
[23] minfi_1.28.3
[24] bumphunter_1.24.5
[25] locfit_1.5-9.1
[26] iterators_1.0.10
[27] foreach_1.4.4
[28] Biostrings_2.50.2
[29] XVector_0.22.0
[30] SummarizedExperiment_1.12.0
[31] DelayedArray_0.8.0
[32] BiocParallel_1.16.5
[33] matrixStats_0.54.0
[34] Biobase_2.42.0
[35] GenomicRanges_1.34.0
[36] GenomeInfoDb_1.18.1
[37] IRanges_2.16.0
[38] S4Vectors_0.20.1
[39] BiocGenerics_0.28.0
[40] dplyr_0.7.8
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'data.table' is missing or broken
2: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'checkmate' is missing or broken
3: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'rlang' is missing or broken
4: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'VariantAnnotation' is missing or broken
5: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'colorspace' is missing or broken
6: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'tibble' is missing or broken
7: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'curl' is missing or broken
8: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'openssl' is missing or broken
>
Ok, thank you. I have the correct file now. I can see the file in the packages i have loaded, however i am still getting the same error as above. I checked the dependencies and all are installed as well. Is there an obvious error that i'm missing?
Could you update all the other packages reported at the end of the R session? (curl, colorspace, tibble, openssl, VariantAnnotation, data.table, checkmate and rlang). Also these errors appearing after the R session information means you have some problems in the installation: do you have all the packages in the same folder and just once? (check the folders
.libPaths())Useful to confirm that at least the Bioconductor packages are consistent, using
BiocManager::valid().