[BioC] random location of duplicate spots and use of limma

[Jason Skelton]

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>
>Hello
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>There are approximately 6000 different genes on the arrays, there are two spots for each gene
>The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances:
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>  Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
>   4.00   32.00   71.00   86.59  135.00  244.00 
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>(Distance here means number of spots between the two duplicates)
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>The function duplicateCorrelation in limma can be used to estimate correlation between within-array duplicates, the methodology is based on the assumption that duplicates are equally spaced. Since this assumption is not fulfilled here does this means that I cannot calculate the correlations and must take the average of the duplicates? Are there some functions to do this in limma or other BioC packages
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Hi ingunn & all

I could be wrong about this but can you get round this in limma by:
normalising the data first(to allow for the physical location on the array)
followed by re-arranging the normalised data so that duplicate genes 
appear next to each other
and therefore have equal spacing ? I.e spacing of 1 or similar.
You obviously have to make new genelists for the  "rearranged" order but 
I can't see any obvious problems with
further analysis such as the linear model fitting etc. If you only have 
two replicates then it should be ok......
I do this routinely but the limma authors might be able to suggest a 
better alternative ?


Jason







>-- 
>--------------------------------
>Jason Skelton
>Pathogen Microarrays
>Wellcome Trust Sanger Institute
>Hinxton
>Cambridge
>CB10 1SA
>
>Tel +44(0)1223 834244 Ext 7123
>Fax +44(0)1223 494919
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