Hi Pan,

maybe there could be some warning if one is subsetting a LumiBatch object which has a detection slot or maybe you could add a remark in Subsection 5.2 of the lumi vignette.

Thanks for your lumi package!
Matthias


----- original message --------

Subject: Re: [BioC] method "[" for class LumiBatch
Sent: Tue, 05 Jun 2007
From: Pan Du

Hi Matthias,

You have noticed the problem of subsetting of presentCount in the featureData of LumiBatch class, but completely solve this problem will spend some time.
The problem of subsetting presentCount involves recalculating the presentCount for the subsetted data. Recalculating the presentCount requires the “detection” slot in the LumiBatch object and the parameters used for calculating the presentCount of the original data. Because the detection slot is optional in the LumiBatch object, the recalculation is impossible in the case of missing detection slot. We will further discuss the solution for this problem and let you know it ASAP.
Thanks for reporting the problem.


Pan


Date: Mon, 4 Jun 2007 11:23:23 +0200 (MEST)
From: "Matthias Kohl" <Matthias.Kohl@stamats.de>
Subject: [BioC] method "[" for class LumiBatch
To: bioconductor@stat.math.ethz.ch
Message-ID: <200706040923.l549NNXj017850@post.webmailer.de>
Content-Type: text/plain; charset="ISO-8859-1"

Hello,

a short question concerning method "[" for class LumiBatch. I'm working with version 1.3.5 of lumi.

Extracting a sub-batch via "[" seems to have no effect on "presentCount" in the slot featureData. 
Shouldn't it be adapted to the sub-batch?

Thanks for any comments!

Best regards
Matthias
 

---------------------------------------------------
Pan Du, PhD
Research Associate / Senior Bioinformatics Analyst
Robert H. Lurie Comprehensive Cancer Center
Northwestern University
676 ST Clair St., #1200
Chicago, IL 60611
Office (312)695-4781
dupan@northwestern.edu
---------------------------------------------------




--- original message end ----

	[[alternative(swapped) HTML version deleted]]

