[BioC] Workflow question in lumi

[Longsi Ran]

Hi, Simon,

Transformation first or normalization first, it is still a question.

I have been using commerce software for years.  GeneTraffic and its sister 
ArrayAssist, for example, typically run normalization first, whether on one 
color or two color data, then Log transformation, before statistic analysis 
(such as F-test).

Sorin Draghici, in his book of "Data Analysis Tools for DNA Microarrays", 
suggested workflow for cDNA microarrays in 8 steps (p.337).  Log 
transformation is the step 7, after several normalizations.

R package "IlluminaGUI" does quantile normalization without Log 
transformation first.

...

I am new to Illumina and R.  Do you have any test data to confirm that your 
workflow is better than others?

Best regards.

Longsi Ran, M.D.




>From: "Simon Lin" <S-Lin2 at northwestern.edu>
>To: "Longsi Ran" <longsiran1126 at hotmail.com>,<dupan at northwestern.edu>
>Subject: Re: [BioC] Workflow question in lumi
>Date: Thu, 31 May 2007 10:46:51 -0500
>
>I am not sure what you are referring to "the normalization should be done 
>on linear scales (using not logged raw data)".
>
>Several microarray textbooks (including Speed; Gentleman; and Baldi) 
>suggest doing transformation (log or others) first, and normalization 
>later; because there are distribution assumptions for most normalization 
>procedures.
>
>I would be interested to find out a paper or reference doing it in the 
>reverse order.
>
>Best regards,
>
>Simon
>
>----- Original Message ----- From: "Longsi Ran" <longsiran1126 at hotmail.com>
>To: <dupan at northwestern.edu>
>Cc: <bioconductor at stat.math.ethz.ch>; <S-Lin2 at northwestern.edu>
>Sent: Thursday, May 31, 2007 8:29 AM
>Subject: [BioC] Workflow question in lumi
>
>
>>Hi,
>>
>>I noticed that your recommended Illumina workflow in lumi is: 1. VST 
>>transformation (including Logarithm).  2, RSN or Quantile normalization. 
>>As most of normalization work on linear expression values, is there a 
>>particular logic to establish normalizing only logged data?  In other 
>>words, Logarithm first, then Normalization, or vice versa?
>>
>>I am looking forward to hearing from you soon.
>>
>>Thanks!
>>
>>Longsi Ran M.D
>>
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>

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