[BioC] HELP! lmFit and duplicateCorrelation
Jenny Drnevich
drnevich at uiuc.edu
Tue Oct 9 23:37:02 CEST 2007
You should NEVER sort the internal components of your MA list
separately! To sort all of them at once, just sort on the MA object itself:
MA2 <- MA[order(MA$genes$ID) , ]
This will keep all the internal components in the same order. You
*really* should start playing around with the objects on your own,
and reading through all the help files instead of immediately asking
questions to the list. This will help you learn R better, and
increase the odds that someone will respond to your question when you
really get stuck.
Good luck,
Jenny
At 04:22 PM 10/9/2007, Tiandao Li wrote:
>Dear Jenny,
>
>After I sorted MA$M and MA$A by MA$genes$ID separately, do I need to sort
>MA$genes by MA$genes$ID or not?
>
>Many Thanks,
>
>Tiandao
>
>On Tue, 9 Oct 2007, Jenny Drnevich wrote:
>
>
> >Thank you for your reply. I have another question if you would help me. If
> >I sort the MA by MA$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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> >
> >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/bioconductor
>Search the archives:
>http://news.gmane.org/gmane.science.biology.informatics.conductor
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
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