[BioC] merged affy 430 A&B

[YBao]

Hi Jim,

Thanks much for sharing your thought. For where I stand, I thought it
would be easier to handle in the downstream analysis if chip A and
chip B could merge into one set of metadata. At least for comparing
that to data from later chip type such as MG430_2.

Best,

Yongde

On Wed, Apr 6, 2011 at 9:50 AM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> Hi Yongde,
>
> On 4/5/2011 11:53 AM, YBao wrote:
>>
>> Hi all,
>>
>> I wonder if someone has done this -- merging the A set and B set of
>> Affy Mouse chip 430 into one data set so as to facilitate further
>> analysis such as lima. Some pointers will be appreciated.
>
> I don't see much to gain here by combining. There is AFAIK not much overlap
> between the two (and you certainly don't want to get into the business of
> combining probesets from different chips). You would gain some small
> precision in the overall variability estimate used in limma, but otherwise
> just running separate analyses seems easiest.
>
> Best,
>
> Jim
>
>
>>
>> Thanks
>>
>> Yongde Bao
>> University of Virginia
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>