[BioC] What wrong with my data using LIMMA

[Adaikalavan Ramasamy]

Gordon, this is a good point that you raise. But can I ask you another,
somewhat harder, question ? 

What should one do when the an arrays fail quality assessment. Do we
simply omit it or can we possible correct for them. The decision to omit
might be the obvious one but it seems a bit wasteful when the the
proportion of arrays is large.

I would be equally happy to hear from others on the list as well.

Regards, Adai



On Tue, 2005-09-06 at 07:22 +1000, Gordon Smyth wrote:
> When  people fail to find differential expression when they expected it, 
> the most common cause is that they have not checked the quality of their 
> data. See the affy, affyPLM and simplyaffy packages for quality assessment 
> steps for Affymetrix data. Perhaps one of the affy people will provide a 
> concise summary. You should always do quality assessment as part of your 
> analysis.
> 
> Gordon
> 
> >Date: Sun, 4 Sep 2005 17:51:05 -0700 (PDT)
> >From: weinong han <hanweinong at yahoo.com>
> >Subject: [BioC] What wrong with my data using LIMMA
> >To: bioconductor at stat.math.ethz.ch
> >
> >Hi. List,
> >
> >17 samples(3 normal samples, 14 NPC tumor samples from different
> >patients)
> > >were used in my Affymetrix microarray experiments. The small size
> > >microarrays were recommmended to be analyzed using LIMMA. After
> >moderated
> > >t statistic, I found the results were not so nice. please see
> >attachment.
> > >
> > >What is wrong with my data? How to do next?
> > >
> > >Any advice and suggestions will be much appreciated.
> > >
> > >I am looking forward to your response
> >
> >
> >
> >Best Regards
> >
> >Han Weinong
> >hanweinong at yahoo.com
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>