[BioC] HELP! lmFit and duplicateCorrelation

[Tiandao Li]

Hello Ido,

        Block   Row     Column  ID      Name
519     4       2       17      37A-C02.g       P00765
531     4       4       17      37A-C02.g       P00765
513     4       1       17      37A-C02.g       P00765

For 37A-C02.g, I only selected the first couple of genes from the topTable 
list, all 4 replicate spots are printed consecutively in the same column.

Thanks for your reply.

Tiandao

On Tue, 9 Oct 2007, Ido M. Tamir wrote:

On Tuesday 09 October 2007 01:20, Tiandao Li wrote:
> Hello,
>
> I had arrays with 4 replicate spots per gene. I used limma package for
> data analysis.
>
> > targets
>
>          SlideNumber FileName Cy3 Cy5   Name
> Field1           1 13617731 WBM  WC Field1
> Field2           2 13617730 WBM  WC Field2
> Field3           3 13617724  WC WBM Field3
> Field4           4 13617627  WC WBM Field4
> Field5           5 13617626 WBM  WC Field5
>
> After read in data, normalization, I used the following codes for
> within-array replicate spots.
>
> design <- modelMatrix(targets, ref="WC")
> corfit <- duplicateCorrelation(MA, design, ndups=4) # A slow computation!
> fit <- lmFit(MA, design, ndups=4, correlation=corfit$consensus,
> method="ls")
> fit2 <- lmFit(MA, design, ndups=4, correlation=corfit$consensus,
> method="robust")

Dear Tiandao,

unless the replicate spots are consecutive you have to give a spacing
argument to indicate what the replicate spots actually are.
If they are randomly spotted on the array, you would have to rearrange
them somehow and then use the appropriate spacing.

519     4       2       17      37A-C02.g       P00765
531     4       4       17      37A-C02.g       P00765

doesn't look as if the replicate spots are one after the other.

HTH best wishes,
ido

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