[BioC] HELP! lmFit and duplicateCorrelation

[Tiandao Li]

Dear Jenny,

I checked the MA$genes, the following is part of the list

1 45Rev2-A03.g
....
25 45Rev2-A03.g
...
49 45Rev2-A03.g

23 rows between 2 replicate spots, so spacing=24?

Thansk,

Tiandao

On Tue, 9 Oct 2007, Jenny Drnevich wrote:

At 09:19 AM 10/9/2007, Tiandao Li wrote:
>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.

This is not the same as consecutively spacing in ROWS, which is what 
the default value of spacing=1 means. Your spacing is probably the 
number of spots per row on the array. Check MA$genes to see how many 
rows of the data matrix separate your duplicates.

Jenny



>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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