Dear list,
 
I have a CGH microarray experiment where I compare male vs. female in each sample (3 technical replicates with dye swaps = 6 samples). So in theory I would expect to see a difference in log2ratios of the X chromosome compared to the autosomes. This experiment is made mainly to assess/optimize the reliability of the protocol and the in-house microarray platform for CGH microarrays experiments.
 
I already used packages in Bioconductor that deal with CGH microarrays but I would also like to have a statistical test to see if there is a significance difference between the mean values of log2ratios from the X chromosome compared to the autosomes. 
I already did a two-sample T-test and a Wilcox.test where the log2ratios for autosomal clones represent the first sample and log2ratios for clones from chromosome X represent the second sample.
 
1 - Should have done another more robust test? Is there any other kind of statistical tests that I can perform to assess the reliability of my experiment (assuming that the pre-processing and normalization is already optimized)?
 
2 - Is it statistical acceptable to average my technical replicates (the average is a weighted average where the arrays with "more quality" have a higher weight) in order to reduce the variance?  
 

Med venlig hilsen / Regards

João Fadista
Ph.d. studerende / Ph.d. student


 	
 	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS	
Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences	
Forskningscenter Foulum / Research Centre Foulum	
Genetik og Bioteknologi / Dept. of Genetics and Biotechnology	
Blichers Allé 20, P.O. BOX 50	
DK-8830 Tjele	
 	
Tel:	 +45 8999 1900	
Direct:	 +45 8999 1900	
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E-mail:	 Joao.Fadista@agrsci.dk <mailto:Joao.Fadista@agrsci.dk> 	
Web:	 www.agrsci.dk <http://www.agrsci.dk/> 	
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