[BioC] Limma final gene expression report

[Ankit Pal]

There are different oliogos of the same gene and
replicates with the same sequence present on the
array.
Splice variants have been mapped to the same Accession
number but I'm working on that to separate out the
same by naming them differently.
-Ankit

--- Sean Davis <sdavis2 at mail.nih.gov> wrote:

> One other question--are these replicate spots (i.e.,
> the same DNA) or 
> different oligos/clones for the same gene?
> 
> Sean
> 
> On May 10, 2005, at 5:59 AM, Ankit Pal wrote:
> 
> > Dear Mick,
> > Thanks a lot for the reply.
> > I am interested in the spots individually but for
> > further analysis of the spots I need a single
> > representative value for each gene.
> > I have looked up the manual, I did not find a way
> to
> > combine replicate spots into a single value.
> > Could you tell me what is the method or which
> section
> > of the manual is it present in.
> > t will be of great help to me.
> > Thank you,
> > -Ankit
> >
> >
> > --- "michael watson (IAH-C)"
> > <michael.watson at bbsrc.ac.uk> wrote:
> >> There are ways of combining replicate spots in
> >> limma, and it is all in the user guide :-)
> >>
> >> However, many people, myself included, prefer
> things
> >> reported on a spot-by-spot basis.  If all
> replicate
> >> spots for a particular gene are reported as
> >> significant, I take that as further proof that i)
> >> the gene is differentially expressed, ii) my
> arrays
> >> are of good quality, iii) my experimental
> procedure
> >> was of good quality.  Think about the case where
> >> only one out of two spots is reported - is that
> >> because one of the spots was of poor quality?  Or
> >> because the values for each spot differ by a lot?
> >> You would lose this valuable information if you
> just
> >> took the average between replicates.
> >>
> >> If you *really* want an average value for each
> spot,
> >> simply take the average M value from the output
> of
> >> toTapble.
> >>
> >> Mick
> >>
> >>
> >> -----Original Message-----
> >> From:	bioconductor-bounces at stat.math.ethz.ch on
> >> behalf of Ankit Pal
> >> Sent:	Tue 10/05/2005 6:15 AM
> >> To:	bioconductor at stat.math.ethz.ch
> >> Cc:	
> >> Subject:	[BioC] Limma final gene expression
> report
> >>
> >> Dear All,
> >> While looking at the Limma user guide, I came
> across
> >> the following example
> >>
> >>> targets <- readTargets("SwirlSample.txt")
> >>> RG <- read.maimages(targets$FileName,
> >> source="spot")
> >>
> >>> RG$genes <- readGAL()
> >>> RG$printer <- getLayout(RG$genes)
> >>> MA <- normalizeWithinArrays(RG)
> >>> MA <- normalizeBetweenArrays(MA)
> >>> fit <- lmFit(MA, design=c(-1,1,-1,1))
> >>> fit <- eBayes(fit)
> >>> options(digits=3)
> >>> topTable(fit, n=30, adjust="fdr")
> >> ID        Name       M    A     t  P.Value    B
> >> control   BMP2      -2.21 12.1 -21.1 0.000357
> 7.96
> >> control   BMP2      -2.30 13.1 -20.3 0.000357
> 7.78
> >> control   Dlx3      -2.18 13.3 -20.0 0.000357
> 7.71
> >> control   Dlx3      -2.18 13.5 -19.6 0.000357
> 7.62
> >> fb94h06 20-L12       1.27 12.0  14.1 0.002067
> 5.78
> >> fb40h07  7-D14       1.35 13.8  13.5 0.002067
> 5.54
> >>
> >> I have omitted a few rows and columns.
> >> Here we see that after all the data
> transformations,
> >> we get an output where the ranking for the probes
> in
> >> an array is  done on the basis of the B value.
> >> Notice that there are reapeating names for genes,
> >> therefore for a set of replicates, within and
> across
> >> arrays, each spot is reported separately as an
> >> individual entity.
> >> In the case of BMP2 from the above example, which
> >> result do I consider?
> >> Is there a way in which I can get a single result
> >> for
> >> a set of replicates.
> >> I am new to this package, so please do let me
> know
> >> if
> >> there is a problem in my understanding the
> concept.
> >> Thank you,
> >> -Ankit
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >>
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
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> 
> 



		
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