[BioC] quality data check

[Wolfgang Huber]

Hi Marcelo,  Gustavo,

Gustavo H. Esteves wrote:
> Hello Marcelo,
> it seems to me that your data wasn't normalized for dye bias. 

I assume you use radioactive labeling on the cDNA membranes - so there 
are no dyes.

Your boxplots look fine to me, almost too clean - the few outliers at 
the bottom and top are perfectly normal, and the quantile normalization 
has indeed achieved its goal of making all distributions look the same.

As Sean suggests, try looking at the scatterplots. Also, if "x" is your 
exprSet or AffyBatch with the data, try the following plot:

cols = colorRampPalette(c("blue", "yellow"))(256)
cc = cor(exprs(x))
image(cc, col=cols)

With this you can find outlier arrays - they are blue.

-----------------

To assess the performance of the normalization, you could calculate the 
F-statistics for each gene (e.g. using "rowFtests" from genefilter 
package) and compare them before and after normalization, or between 
different ways of normalizing / doing quality control.

Best wishes
  Wolfgang
> 
> 2005/5/12, Marcelo Luiz de Laia <mlaia at fcav.unesp.br>:
> 
>>Dear All,
>>
>>We work with cDNA in nylon membranes. We use bioconductor to analyze our
>>data, basically, the packages limma, affy and vsn. The normalizations
>>are made using normalize.quantiles from affy package.
>>
>>However, to verify the quality of the data from this platform is a
>>little complicated with the packages bioconductor. We don't know how to
>>do, if it is possible.
>>
>>Soon, we made one boxplot for each membrane (36 membranes). They are 6
>>treatments with 6 biological repetitions. Each gene was printed 2 times
>>in the membrane.
>>
>>The raw data had been transformed for log into base 2.
>>
>>We are with doubt in relation to the interpretation of the graphs.
>>
>>[not normalized]
>>http://www.lbm.fcav.unesp.br/download/todos.png
>>
>>[normalized]
>>http://www.lbm.fcav.unesp.br/download/todos.norm.png
>>
>>They are:
>>
>>1. it has outliers. The presented amount is very much or is relatively
>>normal for this
>>platform?
>>
>>2. the box is above of line zero (y axis). That is normal? After
>>normalized the data, they are between position 2 and the 3 (y axis).
>>This can happen?
>>
>>We intend to pick up learn with yours commentaries, therefore, you are
>>free to send us any others commentary about the data or quality check on
>>this platform. Yours suggestions is very apreciated.
>>
>>Thanks very much
>>
>>Marcelo
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
> 
> 
> 
> 


-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber