[BioC] What wrong with my data using LIMMA

Gordon Smyth smyth at wehi.edu.au
Mon Sep 5 23:22:54 CEST 2005

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 


>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
> >were used in my Affymetrix microarray experiments. The small size
> >microarrays were recommmended to be analyzed using LIMMA. After
> >t statistic, I found the results were not so nice. please see
> >
> >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

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