[BioC] cDNA microarray Questions

[michael watson (IAH-C)]

As low as 0.5 for pearson and 0.8 for spearman
But I'm not holding up my data as a shining example
Surely if there is a lot of natural variation in the biological system, then you're going to get large variation between biological replicates.
 

-----Original Message-----
From: Naomi Altman [mailto:naomi at stat.psu.edu]
Sent: 28 February 2004 05:20
To: michael watson (IAH-C); 'rwin qian'; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] cDNA microarray Questions


What do you mean by "very low"?

--Naomi

At 04:24 AM 2/27/2004, michael watson (IAH-C) 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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Naomi S. Altman                                814-865-3791 (voice)
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