[BioC] A question about lowess normalization

[Gordon K Smyth]

> Date: Mon, 6 Dec 2004 07:52:44 -0200
> From: Gustavo Henrique Esteves <gesteves at gmail.com>
> Subject: Re: [BioC] A question about lowess normalization
> To: Tony Kowal <askowal at northwestern.edu>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <a79825cf041206015276d69a51 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> There is another way to overcome this type of problem,  that uses a
> smooth background correction to spots that have intensity <
> background. This method was proposed by David Edwards in 2003 and was
> published in Bioinformatics, v 19, pp 825-833.

This and other background correction methods are available in the limma package.

Gordon

> Best regards,
> Gustavo
>
> On Sun, 5 Dec 2004 20:56:15 -0600, Tony Kowal <askowal at northwestern.edu> wrote:
>> Hi All,
>>
>> I have just started using R / Bioconductor within the last couple of
>> weeks to analyze our microarray data.  While attempting to do the Print
>> Tip Lowess normalization on a particular scan, I received the following
>> error, and was unable to proceed with the analysis.  I did a google
>> search for the error message, but I am still unclear about what is
>> wrong with my data.  I have provided the warning I recieved, as well as
>> the list of warning that I requested.  If anyone can provide some
>> suggestions, I will be extremely grateful.
>>
>> There are a fairly large number of NA's in my data.  I am using R 2.0
>> with the most recent version of Bioconductor.  Analysis is being done
>> on a Gateway PC.
>>
>> Thanks in advance,
>> Tony
>>
>> > Error in simpleLoess(y, x, w, span, degree, parametric, drop.square,
>> > normalize,  :
[listing of 50 warnings deleted]
>>
>> Tony Kowal
>> Graduate Student
>>         Department of Cell and Molecular Biology
>> Northwestern University
>> Chisholm Lab
>> 303 E. Chicago Ave.
>> Rm 11-100
>> Chicago, IL 60611
>>
>> e-mail: askowal at northwestern.edu