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$Basename
with values like
SOMETHING/
[Re-posting since messages send to ...@r-project.org bounced for a
period of ~12-14h on Monday Nov 17]
Hi, I've experiences the exact same thing on both a Windows and a
Linux installation. It actually took me a while to realize I didn't
get Bioc devel updates, because I run those in the backgroun
Hi,
At present, the minfi 1.13.1 read.450k.exp function can result in an erroneous
file path when reading in IDAT files using a targets file.
The following line of code can create a path where "base" is repeated as
"targets$Basename" already contains "base" if read.450k.sheet was used to
create
We have created a new experimental data package called 'seqc'. It includes
gene-level read count data generated by the SEQC (SEquencing Quality Control)
project, which is the third stage of the well-known MAQC project (a US FDA
initiative). The SEQC/MAQC-III Consortium produced benchmark RNA-seq
In response to the discussion around plotPCA (
https://stat.ethz.ch/pipermail/bioc-devel/2014-October/006504.html ) ,
the plotPCA generic has been added to the BiocGenerics package. We
encourage package maintainers to update their packages to use the
generic, and seek help on this list if neede
Re-directed from R-devel, where I guess it went by accident.
On 11/18/2014 09:00 AM, Cook, Malcolm wrote:
Hi,
I understand ShortRead::FastqStreamer will read chunks in parallel depending
on the value of ShortRead:::.set_omp_threads
I see this discussed here:
https://stat.ethz.ch/pipermail/bio
I concur on "peaks" vs "scans" or "spectra" issues. One have to run peak
picking algorithm to get peaks out of a spectrum. Therefore I'd vote for
"spectra".
On Tue, Nov 18, 2014 at 12:23 AM, Thomas Lin Pedersen
wrote:
> The coming MSsary package is going to use scans, ions, chroms, peaks,
> li
Dear all,
We are staring to defined generics repeatedly in MS and proteomics
packages (mzR, mzID, MSnID, MSnbase, ...) and thought that these could
be candidates for BiocGenerics. A few suggestions are
setGeneric("psms", function(object, ...) standardGeneric("psms"))
setGeneric("peaks", function
