Proloc and readMSnSet

Question

[ciaki]

Hi all,

I am trying to analyse my data using proloc packaged and I need to somehow read in my data to readMSnSet.

My data is csv files located in my computer but they only way they suggest to load data into R is the following:

> ## The quantitation data, from the original data f1 <- dir(system.file("extdata", package = "pRolocdata"),
>       full.names = TRUE, pattern = "exprsFile.csv") exprsCsv <- read.csv(f1)
> ## Feature meta-data, from the original data f2 <- dir(system.file("extdata", package = "pRolocdata"),
>       full.names = TRUE, pattern = "fdataFile.csv") fdataCsv <- read.csv(f2)
> ## Sample meta-data, a new file f3 <- dir(system.file("extdata", package = "pRolocdata"),
>       full.names = TRUE, pattern = "pdataFile.csv") pdataCsv <- read.csv(f3)

The problem I have when I read my files in using read.csv function instead of the dir(system.file(...) way showing above is that it keeps showing multiple errors.

the problem is that I cannot make this object

tan2009r1 <- readMSnSet(exprsFile = f1,
            featureDataFile = f2,
            phenoDataFile = f3,
            sep = ",")

the error I get after reading my data is this

> > csvfile <- dir(full.names = T,pattern = "f1.csv")
> > csvfile2 <- dir(full.names = T,pattern = "f2.csv")
> > csvfile3 <- dir(full.names = T,pattern = "fractions.csv")


> > tan2009r1 <- readMSnSet(exprsFile = f1, featureDataFile = f2, phenoDataFile = f3,sep = ",")
> >Error in (function (file, header = FALSE, sep = "", quote = "\"'", dec = ".",  :    'file' must be a character string or connection