[BioC] Combining Affymetrix miRNA samples from different arrays

[James W. MacDonald]

Hi Michal,

On 12/9/2010 12:41 PM, Michal Blazejczyk wrote:
> Dear group,
>
> We have a customer who has two datasets obtained using two Affymetrix
> miRNA arrays: miRNA-1_0 and miRNA-1_0_2xgain.  The data are supposed
> to be analyzed together but the problem is that the expression profiles
> from both arrays look very different.  Here's what I did so far:
>   - Normalized both datasets separately using APT.
>     I used APT because to my knowledge there is no CDF package for the
>     2xgain array in Bioconductor.

True, and there probably won't be one until April. I have built the cdf 
package, and it is identical to the miRNA-1_0 package, so you can simply 
change the cdfName of the AffyBatch you get with the 2xgain chips to 
miRNA-1_0 and go from there.


>   - Then I applied an additional quantile normalization step using limma.
> The problem is that even with that, the datasets have very different
> profile patterns (when I do a PCA plot, 96% of the variance is explained
> by the difference in array types).

You won't be able to normalize together. There are things you can do, 
however. The simplest thing would be to assume that the differences 
between sample types are just location differences (rather than scale 
differences), and fit a model with a batch effect. Or you can assume 
scale differences as well, and convert to Z-scores first. Or you can go 
the full meta-analysis route and just use the p-values from separate 
analyses. It all depends on what your goals are, and what the data look 
like.

But more complicated analyses like these lend themselves to help from a 
local statistician rather than help via listserv.

Best,

Jim


>
> I was hoping that maybe someone here has encountered this type of a
> problem before, and would be willing to share his/her thoughts.
>
> Best regards,
>
> Michal Blazejczyk
> FlexArray Lead Developer
> McGill University and Genome Quebec Innovation Centre
> http://genomequebec.mcgill.ca/FlexArray
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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