[BioC] Analisys with MAS5 and affyPLM

Pedro Botías pbotias at bio.ucm.es
Wed Jul 27 11:15:43 CEST 2005

Hi friends,
I would like to carry out a similar analysis of data to which carries out
affylmGUI, but with standard sign data with MAS5, and to carry out a
statistical eBayes to the carried out contrast the same as in affylmGUI.
Serious this correct?
I have tried to carry out it but I find that the data that I obtain are not
correct or distance much of the analysis that I have carried out with GCRMA
in affylmGUI.
These are my chips:
mtl1-diam.CEL        1
mtl1-diam2.CEL      2
mtl1.2.CEL             3
mtl1.CEL                4
wt-diam2.CEL         5
wt-diam3.CEL         6
wt2.CEL                 7
wt3.CEL                 8

I have two you reply of each condition. And I want to carry out the
following contrasts:
 mtl1 vs wt
 mtl1.diam vs mtl1
 wt.diam vs wt

This is the script that I have used for the analysis, noticing limma user's

>strain =
>design = model.matrix(~factor(strain))
>colnames(design) = c("mtl1.diam","mtl1","wt","wt.diam")

Not you if there is something in the design of the analysis that I make bad.
I thank all their help.
Thank you

Pedro Botías Talamantes
Unidad de Genómica
Parque Científico de Madrid-UCM
Facultad CC Biológicas- Planta sótano
Universidad Complutense de Madrid
28040 Madrid
Tel: 91 3945036
FAX 91 3944883
e-mail: pbotias at bio.ucm.es
Web: http://www.ucm.es/info/gyp/genomica/

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