[BioC] HELP! lmFit and duplicateCorrelation

[Tiandao Li]

Dear Jenny,

Thank you for your reply. I have another question if you would help me. If 
I sort the MA by MA$genes$ID, the spacing =1, right? spacing has nothing 
to do with Block, Row, or Column from the gpr file, right?

Thanks so much,

Tiandao

On Tue, 9 Oct 2007, Jenny Drnevich wrote:

At 10:38 AM 10/9/2007, Tiandao Li wrote:
> 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?

Yes.


> 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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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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e-mail: drnevich at uiuc.edu