[BioC] HELP! lmFit and duplicateCorrelation
Al Ivens
alicat at sanger.ac.uk
Tue Oct 9 20:49:44 CEST 2007
Further to Jenny's suggestion,
> summary(MA$genes$ID)
should tell you if the blanks/controls etc are there in more than 4
copies.
hth,
a
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
> Jenny Drnevich
> Sent: 09 October 2007 18:57
> To: Tiandao Li
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] HELP! lmFit and duplicateCorrelation
>
>
>
> >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?
>
> Correct - the spacing is taken from the order in the MA object and
> does not rely on the Block, Row & Column info. Be careful about
> sorting your MA object - as I said before, other spots such as
> buffers and blanks may appear more than 4 times, and may mess up your
> ordered sets of 4. You should always double check to make sure the
> outcome of sorting is what you intended it to be.
>
> Jenny
>
>
>
>
> >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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> > > >
> > > >_______________________________________________
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> > > _______________________________________________
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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
> >
> >330 ERML
> >1201 W. Gregory Dr.
> >Urbana, IL 61801
> >USA
> >
> >ph: 217-244-7355
> >fax: 217-265-5066
> >e-mail: drnevich at uiuc.edu
>
> 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
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/biocondu> ctor
> Search the
> archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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