Dear Oosting and Dr. Smyth:

 

After I tried my regular spacing microarray data, I found that the common
coefficient after order with spacing =1 is different from the coefficient
with original spacing without order. And the difference is big, the first
one with order is 0.5618, the second one without order is 0.1711. Also the
B-statistics based on first one is only half of the value of the
B-statistics of the second one. Could you be kind enough to tell me why this
happens and is there some other good way can solve this irregular spacing
problem?

 

Thank you very much,

 

Hua Weng

 

  _____  

From: Oosting, J. (PATH) [mailto:J.Oosting@lumc.nl] 
Sent: Monday, January 23, 2006 3:50 PM
To: Hua Weng; Gordon Smyth; BioC Mailing List
Subject: RE: [BioC] limma: irregular spacing between within-array replicates

 

After normalization, which could rely on the chip layout, you can order your
data by gene, and assume a spacing of 1
i.e.
MA<-MA[order(RG$genes[,"Name"]),]
corfit <- duplicateCorrelation(MA, ndups=4, spacing=1)

this assumes that:
- there is a  Name column in the gens slot that contains the same value for
each replicate spot
- each gene is replicated exactly 4 times
- if multiple probes are used for a gene they have different names

-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Hua Weng
Sent: Mon 23-Jan-06 9:22 PM
To: 'Gordon Smyth'; 'BioC Mailing List'
Subject: Re: [BioC] limma: irregular spacing between within-array replicates

Hi, Dr. Smyth and Bioconductor mailing list:



Dr. Smyth, Thank you very much for making such a nice package, limma, for
microarray analysis.



I have a question for irregular spacing for within-array replicates. I have
four technical replicates on one array, but the spacing between them is not
regular. The spacing between the first and second replicates is 16, the
spacing between the second and third is 176, and the spacing between the
third and the fourth is 16 again. How can I calculate correlation for within
array replicates based on irregular spacing to make full use of within array
replicates?



I highly appreciate any suggestions and comments.



Hua Weng

Microarray Core Facility

Oklahoma State University


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