Dear developers of minfi,
I have a few suggestions for minfi:
1) In a few analyses with >500 samples we noticed that often the number of
PCs should be larger than the default of 2 for functional normalization.
Now we extract some code from minfi, not exported, using the triple colon
operator, to
Dear all,
Should I worry about not yet updated package sources/binaries in devel:
Package Source MethylAid_1.5.3.tar.gz
Windows Binary None
Mac OS X 10.6 (Snow Leopard) MethylAid_1.3.1.tgz
Mac OS X 10.9 (Mavericks) MethylAid_1.5.3.tgz
For example, no binary for windows and old so
Ok that is clear!
Thanks,
Maarten
On Thu, Mar 31, 2016 at 5:09 PM, Dan Tenenbaum
wrote:
> There were no windows build results yesterday, and Snow Leopard builds
> stopped some time ago. So nothing needs to be done.
> Dan
>
>
> - Original Message -
> > Fr
Dear all,
I'm struggling with using git and the Bioconductor SVN repo of my packages.
For example, I have a package in devel (bacon) and managed to push changes
to the svn/trunk of my package using the steps described at:
https://www.bioconductor.org/developers/how-to/git-mirrors/
following sce
Dear all,
My package MethylAid does not pass check on moscato2.
I got
"Error in while (m%/%128 == 1) { : argument is of length zero
Calls: summarize ... readIDAT_nonenc -> lapply -> FUN -> readField ->
readString"
the summarize function calls read.metharray.exp from minfi which calls
readIDAT/r
ckages:
>> > >> [1] illuminaio_0.13.1
>> > >> [2] minfiData_0.13.0
>> > >> [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
>> > >> [4] IlluminaHumanMethylation450kmanifest_0.4.0
>> > >> [5] minfi_1.17.10
>&
minfi and illuminaio builds
> without problems on Windows.
>
> Kasper
>
> On Tue, Apr 12, 2016 at 2:53 AM, Maarten van Iterson
> wrote:
>
>> Dear Dan and Henrik,
>>
>> Thank you for looking into this!
>>
>> So if I understand correctly the check error
biorxiv (
http://biorxiv.org/content/early/2016/05/27/055772).
Kind regards,
Maarten van Iterson
[[alternative HTML version deleted]]
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Bioc-devel@r-project.org mailing list
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ailable in devel, so
>> advertising on the support site would just lead to disappointment.
>>
>> Open to revised policies / suggestions, though.
>>
>> Martin
>>
>>
>>> Jim
>>>
>>>
>>>
>>> On Thu, Jun 9, 2016 at
Dear list,
Combining SummarizedExperiment object, containing a DNAStringSet in the
rowData seems not to work properly. If I cbind two SummarizedExperiment
objects, which I know are identical, an error is reported:
Error in FUN(X[[i]], ...) (from #2) :
column(s) 'sourceSeq' in ‘mcols’ are duplic
27;ll fix the "cbind" and "rbind" methods for
> SummarizedExperiment to work around this problem.
>
> Thanks for the report.
>
> H.
>
>
> On 04/03/2017 12:58 AM, Maarten van Iterson wrote:
>
>> Dear list,
>>
>> Combining SummarizedExpe
Dear all,
SummarizedExperiment and matrixStats both contain a method/function called
rowRanges one operates on a SummarizedExperiment-object the other on a
matrix. matrixStats is required by SummarizedExperiment, or a package it is
depending on, so rowRanges is masked when loading SummarizedExperi
nt Carey wrote:
>
>> I am sure there are better responses to come, but here are a few initial
>> comments.
>>
>> On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson
>> wrote:
>>
>> Dear all,
>>>
>>> SummarizedExperiment and matrix
Dear all,
I've created a package that contains one vignette showing its core
functionality that I would like to be processed by the build-system and two
other vignettes showing more comprehensive examples, e.g. including
downloading publicly available data from GEO and 1000G vcfs which take too
mu
Dear all,
Our new package, omicsPrint, has been accepted and added to the
bioconductor build system but is not passing through on any system. Locally
we are able to build install and execute the vignette. We have tried
several things without success.
The current error we got for version 0.99.29 o
t your vignette is pointing to a package that doesn't exist
> in the build system.
>
> Please reference `package = "brgedata"` instead.
>
> Regards,
> Marcel
>
>
> *Note. Apologies if you've received this email twice.
>
> On 12/13/2017 02:09 P
Regards,
>
> Marcel
>
>
>
> On 12/13/2017 03:25 PM, Maarten van Iterson wrote:
>
> Hi Marcel,
>
> Thanks for your help, do you mean I should add "bgredata" to our DESCR
> file? omicsPrint should not depend on it?
>
> This sessionInfo when omicsPrint
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