[BioC] cDNA microarray Questions

[rwin qian]

I used the Spearman Rank Correlation Coefficients. 
 
One thing that I am not sure about is how to delete low quality genes after the normalization, especially for one spot-one gene in each array.
Any insights from you will be appreciated!
 
Darwin
 
 

"michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> wrote:
>The correlation coefficients are very low. Is that the normal case? 
>Do I need to delete some poor quality genes before any analysis and 
>what rule should I use? 

Which correlation coefficient are you using? I regularly see very low pearson correlation coefficients between biological replicates but that can be put down to natural biological variation - no two organisms are the same, right? BUT if you start seeing low correlations between technical replicates (e.g. replicate samples from the same animal/tissue/organ/whatever) then that indicates that you have a lot of variation in your technology, which is bad.

ON another note, I always find the Spearman Rank Correlation Coefficients to be much higher.

Mick

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