Problem with working with "methAnalysis" package in R

Question

[nazaninhoseinkhan]

Dear all,

I want to analyze microarray methylation data to find differentially methylated regions.

First I tried to work with Galaxy, but I did not know how can I add required tools to my list of tools in Galaxy.

Someone advise me to use R for this analysis. I found "methyAnalysis" package for this purpose.

However I get these lines of errors when trying to load package:

Error : Function found when exporting methods from the namespace ‘Biostrings’ which is not S4 generic: ‘compare’
In addition: Warning messages:
1: multiple methods tables found for ‘fileName’ 
2: multiple methods tables found for ‘organism’ 
3: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘methylumi’ 
4: no function found corresponding to methods exports from ‘Biostrings’ for: ‘encoding’, ‘splitAsListReturnedClass’ 
Error: package or namespace load failed for ‘methyAnalysis’
>

can anyone help me to solve this problem?

or do you know any other reliable tools that I can use to do methylation analysis.

Thank u in advance

Nazanin

[Persistent LABS]

what's your sessionInfo() ?

Also try to restart R and reload methyAnalysis package alone. Sometimes already loaded objects in workspace can conflict with current loadings.

Also u can try minfi package. This might help. http://kasperdanielhansen.github.io/genbioconductor/html/minfi.html

Thanks

Priyabrata

Persistent LABS

[nazaninhoseinkhan]

My sessioninfo():

local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) Loading required package: grid Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit

Loading required package: IRanges Loading required package: S4Vectors Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: org.Hs.eg.db Loading required package: AnnotationDbi

Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite' In addition: Warning messages: 1: multiple methods tables found for ‘fileName’ 2: multiple methods tables found for ‘organism’ 3: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘methylumi’ Error: package or namespace load failed for ‘methyAnalysis’

I tried minfi too, but there exists the same problem. It seems there is something wrong with RSQLite.

Thanks for the help

Nazanin