Hello all, 

I am new to  Methylation data analysis and having problem in importing data in minfi package- 

After  targets <-read.450k.sheet(baseDir, pattern = "csv$"),  it reads the data sample sheet which has basic Sample_name, Slide etc, I get error in Basename column name ( which is not there in my sample sheet). 

The sample sheets of my other datasets did not have any specific "Basename" column and run fine, but while importing this data it reads Basename column with missing path - 

                                                Basename  Array       Slide
1 E:/10003885002/10003885002_R01C01 R01C01 10003885002
2                                            character(0) R02C01 10003885002

Due to these character(0) the RgSet also gives error : 

The following specified files do not exist:character(0)_Grn.idat

Can anyone please tell why I am getting character(0) under Basename?

can I manually add a Basename column with all paths in my sample sheet?

Do I need to add a Basename column in sample sheet, with path information for each sample? I am not able to find any information anywhere. 

please help!

When you post a question, please use the 'Question' type, rather than 'Tutorial'. As the name might suggest, a Tutorial post is intended to provide a tutorial, rather than ask a question.

The Basename column is generated programmatically, by looking at information in your SampleSheet.csv and then inferring the file name for the corresponding Grn.idat file. In your case, the expectation is that there will be a file

E:/10003885002/10003885002_R02C01_Grn.idat

and when it isn't found, you get a character(0) returned. So you are missing at least one idat file, so you need to figure out why you are missing raw data files.

Thanks James for your reply...I am also stuck at this point. I ran 4 chips in 2sets...when I am trying to read the chip data for the first set...everything is going fine...but when I tried to read data from all the four chips...the basename is showing "Character(0)".

As you mentioned I individually checked for all the idat files and not a single one was missing. At this point please help me how should I proceed? Shall I prepare a target file in .txt format and read it in R?

I know the reason eventually, please see the following script which was used by ChAMP or some other package to read and creat SampleSheet.csv. 

 read.metharray.sheet()

function (base, pattern = "csv$", ignore.case = TRUE, recursive = TRUE,
    verbose = TRUE)
{
    readSheet <- function(file) {
        dataheader <- grep("^\\[DATA\\]", readLines(file), ignore.case = TRUE)
        if (length(dataheader) == 0)
            dataheader <- 0
        df <- read.csv(file, stringsAsFactor = FALSE, skip = dataheader)
        if (length(nam <- grep("Sentrix_Position", names(df),
            ignore.case = TRUE, value = TRUE)) == 1) {
            df$Array <- as.character(df[, nam])
            df[, nam] <- NULL
        }
        if (length(nam <- grep("Array[\\._]ID", names(df), ignore.case = TRUE,
            value = TRUE)) == 1) {
            df$Array <- as.character(df[, nam])
            df[, nam] <- NULL
        }
        if (!"Array" %in% names(df))
            warning(sprintf("Could not infer array name for file: %s",
                file))
        if (length(nam <- grep("Sentrix_ID", names(df), ignore.case = TRUE,
            value = TRUE)) == 1) {
            df$Slide <- as.character(df[, nam])
            df[, nam] <- NULL
        }
        if (length(nam <- grep("Slide[\\._]ID", names(df), ignore.case = TRUE,
            value = TRUE)) == 1) {
            df$Slide <- as.character(df[, nam])
            df[, nam] <- NULL
        }
        if (!"Slide" %in% names(df))
            warning(sprintf("Could not infer slide name for file: %s",
                file))
        else df[, "Slide"] <- as.character(df[, "Slide"])
        if (length(nam <- grep("Plate[\\._]ID", names(df), ignore.case = TRUE,
            value = TRUE)) == 1) {
            df$Plate <- as.character(df[, nam])
            df[, nam] <- NULL
        }
        for (nam in c("Pool_ID", "Sample_Plate", "Sample_Well")) {
            if (nam %in% names(df)) {
                df[[nam]] <- as.character(df[[nam]])
            }
        }
        if (!is.null(df$Array)) {
            patterns <- sprintf("%s_%s_Grn.idat", df$Slide, df$Array)
            allfiles <- list.files(dirname(file), recursive = recursive,
                full.names = TRUE)
            basenames <- sapply(patterns, function(xx) grep(xx,
                allfiles, value = TRUE))
            names(basenames) <- NULL
            basenames <- sub("_Grn\\.idat", "", basenames, ignore.case = TRUE)
            df$Basename <- basenames
        }
        df
    }
    if (!all(file.exists(base)))
        stop("'base' does not exists")
    info <- file.info(base)
    if (!all(info$isdir) && !all(!info$isdir))
        stop("'base needs to be either directories or files")
    if (all(info$isdir)) {
        csvfiles <- list.files(base, recursive = recursive, pattern = pattern,
            ignore.case = ignore.case, full.names = TRUE)
        if (verbose) {
            message("[read.metharray.sheet] Found the following CSV files:\n")
            print(csvfiles)
        }
    }
    else csvfiles <- list.files(base, full.names = TRUE)
    dfs <- lapply(csvfiles, readSheet)
    namesUnion <- Reduce(union, lapply(dfs, names))
    df <- do.call(rbind, lapply(dfs, function(df) {
        newnames <- setdiff(namesUnion, names(df))
        newdf <- matrix(NA, ncol = length(newnames), nrow = nrow(df),
            dimnames = list(NULL, newnames))
        cbind(df, as.data.frame(newdf))
    }))
    df
}

read.450k() throws the character(0)_Grn.idat error because it couldn't find the file specified in the spreadsheet.

One of the most common reason is due to sample sheet format. Look for trailing space or illegal characters in your csv file.