Previously I have successfully analyzed this data set using RnBeads.
I have been asked to return to my dataset and remove two subjects' data from the analysis. I have followed the directions closely to affect this modification and resubmitted the job. But it repeatedly failed (see below).
So, I have reinstalled the latest R package (3.2.2) via Bioconductor, and reinstalled RnBeads but I get the same error messages. I have run out of ideas.
Below is the code and returns:
> setwd("E:/NIDAMethylData/NIDA06")
> data.dir<-"E:/NIDAMethylData/NIDA06"
> idat.dir <- file.path(data.dir, "")
> sample.annotation <- file.path(data.dir, "NIDA_06samplesheet.csv")
> data.source <- c(idat.dir, sample.annotation)
> analysis.dir <- "E:/NIDAMethylData/NIDA06/20150904test01"
> report.dir <- file.path(analysis.dir, "reports")
> result <- rnb.run.import(data.source=data.source, data.type="infinium.idat.dir", dir.reports=report.dir)
2015-09-04 09:26:31 0.3 STATUS STARTED Loading Data
2015-09-04 09:26:31 0.3 INFO Number of cores: 1
2015-09-04 09:26:32 0.3 INFO Loading data of type "infinium.idat.dir"
2015-09-04 09:26:32 0.3 STATUS STARTED Loading Data from IDAT Files
2015-09-04 09:26:32 0.3 INFO Added column barcode to the provided sample annotation table
2015-09-04 09:28:56 0.5 STATUS COMPLETED Loading Data from IDAT Files
2015-09-04 09:29:36 0.4 STATUS Loaded data from E:/NIDAMethylData/NIDA06
2015-09-04 09:29:43 1.3 STATUS Added data loading section to the report
2015-09-04 09:29:45 1.1 STATUS Loaded 96 samples and 485577 sites
2015-09-04 09:29:45 1.1 INFO Output object is of type RnBeadRawSet
2015-09-04 09:29:49 1.5 STATUS COMPLETED Loading Data
> rnb.set <- result$rnb.set
> rnb.set2 <- remove.samples(rnb.set, samples(rnb.set)[c(24, 36)])
> setdiff(samples(rnb.set), samples(rnb.set2))
[1] "95" "96"
> rnb.options(filtering.sex.chromosomes.removal=TRUE, identifiers.column="Sample_Name")
> rnb.run.analysis(dir.reports=report.dir, sample.sheet=sample.annotation, rnb.set2)
2015-09-04 09:31:26 1.1 STATUS STARTED RnBeads Pipeline
2015-09-04 09:31:27 1.1 INFO Initialized report index and saved to index.html
2015-09-04 09:31:27 1.1 STATUS STARTED Loading Data
2015-09-04 09:31:27 1.1 INFO Number of cores: 1
2015-09-04 09:31:27 1.1 INFO Loading data of type "idat.dir"
Error in as.list.default(data.source) :
no method for coercing this S4 class to a vector
>