I was surprised to see that sequence lengths weren't set in the
transcriptDb object TxDb.Athaliana.BioMart.plantsmart19 (I
checked TxDb.Athaliana.BioMart.plantsmart21 in devel too, and it had the
same issue). This seems like something that would be set (though maybe
TranscriptDb objects created fro
edgeR knows about LargeDataObject. It's your package that doesn't.
Gordon
On Fri, 27 Jun 2014, Dario Strbenac wrote:
Hello,
I never explicitly use that class in my function. I did debugging and realised
what the problem is. DGEList is part of class hierarchy and it inherits from
the supe
Hello,
I never explicitly use that class in my function. I did debugging and realised
what the problem is. DGEList is part of class hierarchy and it inherits from
the superclass LargeDataObject
> showClass("DGEList")
Class "DGEList" [package "edgeR"]
Slots:
Name: .Data
Class: li
After some thought, I've decided to import the LargeDataClass as you've
requested, but I have to say that some of your message doesn't make a lot
of sense to me.
The class of your data object looks weird. Is this really a valid class?
glmFit() doesn't have a method for the LargeDataObject cla
Thank you. I made that change to the edgeR source code and reinstalled it, but
I get another error further in my function :
Error in UseMethod("glmFit") :
no applicable method for 'glmFit' applied to an object of class "c('DGEList',
'list', 'LargeDataObject', 'vector')"
This is because of La
Many thanks to Dan and Kieran O'Neill!
I will adjust my plan according to the estimated timeline.
Xiaobei
On 6/26/2014 5:19 PM, Kieran O'Neill wrote:
> After the initial response, the package will be sent on to a reviewer,
> who will usually respond within a week or two, but could take longer.
>
Date: Thu, 26 Jun 2014 04:00:11 +
From: Dario Strbenac
To: "bioc-devel@r-project.org"
Subject: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called
From A Package
Hello,
I am writing a package that has a function that uses estimateGLMRobustDisp,
leading to an error :
Err
- Original Message -
> From: "Xiaobei Zhao"
> To: bioc-devel@r-project.org
> Sent: Thursday, June 26, 2014 5:20:31 AM
> Subject: [Bioc-devel] New package submission process
>
> Hi everyone,
>
> I am about to submit a new package at Bioconductor. I have followed
> the
> instructions lin
Hi Dario,
Isn't an easier fix to simply add
ImportFrom(limma, loessFit)
in your NAMESPACE file?
Best,
Jim
On 6/26/2014 12:00 AM, Dario Strbenac wrote:
Hello,
I am writing a package that has a function that uses
estimateGLMRobustDisp, leading to an error :
Error in dispBinTrend(y, design,
Hi everyone,
I am about to submit a new package at Bioconductor. I have followed the
instructions linked below to prepare my package,
http://master.bioconductor.org/developers/package-guidelines/
Early this week, I sent an initial request according to the contact
information listed at
http:/
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