[Bioc-devel] Error when using read.450k.exp from minfi 1.13.1

Kasper Daniel Hansen khansen at jhsph.edu
Wed Nov 19 03:54:41 CET 2014

This was reported a while ago by Dan Tenenbaum, forgotten about by me and
fixed tonight in minfi v1.13.2

The previous use of the read.450k.exp function, where there was both a
  base = SOMETHING
and a targets object (created by read.450k.sheet) with a targets$Basename
with values like
is no longer support (it used to be that the base argument was ignored).
User now just have to do

sheet = read.450k.sheet(ARGS)
rgset = read.450k.exp(targets = sheet)

We now support giving a base argument in case targets$Basename does not
contain the full path.

And this time I hope it works....


On Tue, Nov 18, 2014 at 7:38 PM, Jovana Maksimovic <
jovana.maksimovic at mcri.edu.au> wrote:

> Hi,
> At present, the minfi 1.13.1 read.450k.exp function can result in an
> erroneous file path when reading in IDAT files using a targets file.
> The following line of code can create a path where "base" is repeated as
> "targets$Basename" already contains "base" if read.450k.sheet was used to
> create "targets":
>         files <- file.path(base, targets$Basename)
> This results in an error when  trying to read in the files:
>         rgSet <- read.450k(files, extended = extended, verbose = verbose)
> This is an example of the error:
> Error: processing vignette 'minfi.Rnw' failed with diagnostics:
> chunk 7 (label = paths)
> Error in read.450k(files, extended = extended, verbose = verbose) :
>   The following specified files do not
> exist:/home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R02C02_Grn.idat,
> /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R04C01_Grn.idat,
> /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R05C02_Grn.idat,
> /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646053/5723646053_R04C02_Grn.idat,
> /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat,
> /home/biocbuild/bbs-3.1-bioc/R
> Execution halted
> This is currently affecting the development version of minfi and any other
> packages that are using minfi functions to read in methylation data.
> Regards,
> Jovana Maksimovic
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