I can't help feeling that running 55 contrasts is 'dredging' your
data.
Why not run 11 contrasts each group against everything else?
Stephen Henderson
Wolfson Institute for Biomedical Research
Cruciform Buildging, Gower Street
University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Artur
Veloso
Sent: 18 September 2007 15:50
To: Bioconductor List
Subject: Re: [BioC] analysis of 70 groups for differential expression
Hi,
I have a question very similar to the one described here.
I have samples from 11 environmental groups, so there is no control in
the
experiment. Therefore, there are 55 comparisons that can be made and
are
of
interest in the experiment.
My approach before reading this was to run all comparisons
independently
from each other, using makeContrasts, contrasts.fit,etc 55 times, and
then
use decideTests to pull out the differently expressed genes. But I
believe
that this is incorrect, since I am not adjusting the p-value for these
55
tests.
The new approach that I tried was to run all the comparisons together
(use
makeContrasts just once) and then use decideTests and use each column
of
the
TestResult matrix to extract DE genes for that specific comparison.
But, when I compared TestResult matrix columns from the same
comparisons
run
under the different methods described above I found no differences.
But
I
did not look into the q-values or the lods.
Was I wrong to run the 55 comparisons separately? Is the new approach
more
appropriate?
Thank you very much for the help!
Artur B. Veloso
Masters in Marine Biology Candidate
College of Charleston, South Carolina, USA
############ 55 ANOVAs
site.design <- read.csv("gill_site_contrast.csv")
site.design[is.na(site.design)] <- 0
oyster.site.correlation <-
duplicateCorrelation(oyster.red.vsn,site.design
,ndups=2,spacing=1)
oyster.site.lm <- lmFit(oyster.red.vsn,site.design
,ndups=2,spacing=1,correlation=oyster.site.correlation$consensus.corre
la
tion
)
#guerin.vs.village
guerin.vs.village.contrast <- makeContrasts(guerin-village,levels=
site.design)
guerin.vs.village.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.village.contrast)
guerin.vs.village.ebayes <- eBayes(guerin.vs.village.fit)
#guerin.vs.duplin
guerin.vs.duplin.contrast <-
makeContrasts(guerin-duplin,levels=site.design)
guerin.vs.duplin.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.duplin.contrast)
guerin.vs.duplin.ebayes <- eBayes(guerin.vs.duplin.fit)
#guerin.vs.oakdale
guerin.vs.oakdale.contrast <- makeContrasts(guerin-oakdale,levels=
site.design)
guerin.vs.oakdale.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.oakdale.contrast)
guerin.vs.oakdale.ebayes <- eBayes(guerin.vs.oakdale.fit)
#guerin.vs.postell
guerin.vs.postell.contrast <- makeContrasts(guerin-postell,levels=
site.design)
guerin.vs.postell.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.postell.contrast)
guerin.vs.postell.ebayes <- eBayes(guerin.vs.postell.fit)
#guerin.vs.burnett
guerin.vs.burnett.contrast <- makeContrasts(guerin-burnett,levels=
site.design)
guerin.vs.burnett.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.burnett.contrast)
guerin.vs.burnett.ebayes <- eBayes(guerin.vs.burnett.fit)
#guerin.vs.new.market
guerin.vs.new.market.contrast <- makeContrasts(guerin-
new.market,levels=
site.design)
guerin.vs.new.market.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.new.market.contrast)
guerin.vs.new.market.ebayes <- eBayes(guerin.vs.new.market.fit)
#guerin.vs.hewletts
guerin.vs.hewletts.contrast <- makeContrasts(guerin-hewletts,levels=
site.design)
guerin.vs.hewletts.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.hewletts.contrast)
guerin.vs.hewletts.ebayes <- eBayes(guerin.vs.hewletts.fit)
#guerin.vs.masonboro
guerin.vs.masonboro.contrast <- makeContrasts(guerin-masonboro,levels=
site.design)
guerin.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.masonboro.contrast)
guerin.vs.masonboro.ebayes <- eBayes(guerin.vs.masonboro.fit)
#guerin.vs.whiskey
guerin.vs.whiskey.contrast <- makeContrasts(guerin-whiskey,levels=
site.design)
guerin.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.whiskey.contrast)
guerin.vs.whiskey.ebayes <- eBayes(guerin.vs.whiskey.fit)
#guerin.vs.james.island
guerin.vs.james.island.contrast <-
makeContrasts(guerin-james.island,levels=
site.design)
guerin.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
guerin.vs.james.island.contrast)
guerin.vs.james.island.ebayes <- eBayes(guerin.vs.james.island.fit)
#village.vs.duplin
village.vs.duplin.contrast <- makeContrasts(village-duplin,levels=
site.design)
village.vs.duplin.fit <- contrasts.fit(oyster.site.lm,
village.vs.duplin.contrast)
village.vs.duplin.ebayes <- eBayes(village.vs.duplin.fit)
#village.vs.oakdale
village.vs.oakdale.contrast <- makeContrasts(village-oakdale,levels=
site.design)
village.vs.oakdale.fit <- contrasts.fit(oyster.site.lm,
village.vs.oakdale.contrast)
village.vs.oakdale.ebayes <- eBayes(village.vs.oakdale.fit)
#village.vs.postell
village.vs.postell.contrast <- makeContrasts(village-postell,levels=
site.design)
village.vs.postell.fit <- contrasts.fit(oyster.site.lm,
village.vs.postell.contrast)
village.vs.postell.ebayes <- eBayes(village.vs.postell.fit)
#village.vs.burnett
village.vs.burnett.contrast <- makeContrasts(village-burnett,levels=
site.design)
village.vs.burnett.fit <- contrasts.fit(oyster.site.lm,
village.vs.burnett.contrast)
village.vs.burnett.ebayes <- eBayes(village.vs.burnett.fit)
#village.vs.new.market
village.vs.new.market.contrast <-
makeContrasts(village-new.market,levels=
site.design)
village.vs.new.market.fit <- contrasts.fit(oyster.site.lm,
village.vs.new.market.contrast)
village.vs.new.market.ebayes <- eBayes(village.vs.new.market.fit)
#village.vs.hewletts
village.vs.hewletts.contrast <- makeContrasts(village-hewletts,levels=
site.design)
village.vs.hewletts.fit <- contrasts.fit(oyster.site.lm,
village.vs.hewletts.contrast)
village.vs.hewletts.ebayes <- eBayes(village.vs.hewletts.fit)
#village.vs.masonboro
village.vs.masonboro.contrast <- makeContrasts(village-
masonboro,levels=
site.design)
village.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
village.vs.masonboro.contrast)
village.vs.masonboro.ebayes <- eBayes(village.vs.masonboro.fit)
#village.vs.whiskey
village.vs.whiskey.contrast <- makeContrasts(village-whiskey,levels=
site.design)
village.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
village.vs.whiskey.contrast)
village.vs.whiskey.ebayes <- eBayes(village.vs.whiskey.fit)
#village.vs.james.island
village.vs.james.island.contrast <- makeContrasts(village-james.island
,levels=site.design)
village.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
village.vs.james.island.contrast)
village.vs.james.island.ebayes <- eBayes(village.vs.james.island.fit)
#duplin.vs.oakdale
duplin.vs.oakdale.contrast <- makeContrasts(duplin-oakdale,levels=
site.design)
duplin.vs.oakdale.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.oakdale.contrast)
duplin.vs.oakdale.ebayes <- eBayes(duplin.vs.oakdale.fit)
#duplin.vs.postell
duplin.vs.postell.contrast <- makeContrasts(duplin-postell,levels=
site.design)
duplin.vs.postell.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.postell.contrast)
duplin.vs.postell.ebayes <- eBayes(duplin.vs.postell.fit)
#duplin.vs.burnett
duplin.vs.burnett.contrast <- makeContrasts(duplin-burnett,levels=
site.design)
duplin.vs.burnett.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.burnett.contrast)
duplin.vs.burnett.ebayes <- eBayes(duplin.vs.burnett.fit)
#duplin.vs.new.market
duplin.vs.new.market.contrast <- makeContrasts(duplin-
new.market,levels=
site.design)
duplin.vs.new.market.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.new.market.contrast)
duplin.vs.new.market.ebayes <- eBayes(duplin.vs.new.market.fit)
#duplin.vs.hewletts
duplin.vs.hewletts.contrast <- makeContrasts(duplin-hewletts,levels=
site.design)
duplin.vs.hewletts.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.hewletts.contrast)
duplin.vs.hewletts.ebayes <- eBayes(duplin.vs.hewletts.fit)
#duplin.vs.masonboro
duplin.vs.masonboro.contrast <- makeContrasts(duplin-masonboro,levels=
site.design)
duplin.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.masonboro.contrast)
duplin.vs.masonboro.ebayes <- eBayes(duplin.vs.masonboro.fit)
#duplin.vs.whiskey
duplin.vs.whiskey.contrast <- makeContrasts(duplin-whiskey,levels=
site.design)
duplin.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.whiskey.contrast)
duplin.vs.whiskey.ebayes <- eBayes(duplin.vs.whiskey.fit)
#duplin.vs.james.island
duplin.vs.james.island.contrast <-
makeContrasts(duplin-james.island,levels=
site.design)
duplin.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
duplin.vs.james.island.contrast)
duplin.vs.james.island.ebayes <- eBayes(duplin.vs.james.island.fit)
#oakdale.vs.postell
oakdale.vs.postell.contrast <- makeContrasts(oakdale-postell,levels=
site.design)
oakdale.vs.postell.fit <- contrasts.fit(oyster.site.lm,
oakdale.vs.postell.contrast)
oakdale.vs.postell.ebayes <- eBayes(oakdale.vs.postell.fit)
#oakdale.vs.burnett
oakdale.vs.burnett.contrast <- makeContrasts(oakdale-burnett,levels=
site.design)
oakdale.vs.burnett.fit <- contrasts.fit(oyster.site.lm,
oakdale.vs.burnett.contrast)
oakdale.vs.burnett.ebayes <- eBayes(oakdale.vs.burnett.fit)
#oakdale.vs.new.market
oakdale.vs.new.market.contrast <-
makeContrasts(oakdale-new.market,levels=
site.design)
oakdale.vs.new.market.fit <- contrasts.fit(oyster.site.lm,
oakdale.vs.new.market.contrast)
oakdale.vs.new.market.ebayes <- eBayes(oakdale.vs.new.market.fit)
#oakdale.vs.hewletts
oakdale.vs.hewletts.contrast <- makeContrasts(oakdale-hewletts,levels=
site.design)
oakdale.vs.hewletts.fit <- contrasts.fit(oyster.site.lm,
oakdale.vs.hewletts.contrast)
oakdale.vs.hewletts.ebayes <- eBayes(oakdale.vs.hewletts.fit)
#oakdale.vs.masonboro
oakdale.vs.masonboro.contrast <- makeContrasts(oakdale-
masonboro,levels=
site.design)
oakdale.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
oakdale.vs.masonboro.contrast)
oakdale.vs.masonboro.ebayes <- eBayes(oakdale.vs.masonboro.fit)
#oakdale.vs.whiskey
oakdale.vs.whiskey.contrast <- makeContrasts(oakdale-whiskey,levels=
site.design)
oakdale.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
oakdale.vs.whiskey.contrast)
oakdale.vs.whiskey.ebayes <- eBayes(oakdale.vs.whiskey.fit)
#oakdale.vs.james.island
oakdale.vs.james.island.contrast <- makeContrasts(oakdale-james.island
,levels=site.design)
oakdale.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
oakdale.vs.james.island.contrast)
oakdale.vs.james.island.ebayes <- eBayes(oakdale.vs.james.island.fit)
#postell.vs.burnett
postell.vs.burnett.contrast <- makeContrasts(postell-burnett,levels=
site.design)
postell.vs.burnett.fit <- contrasts.fit(oyster.site.lm,
postell.vs.burnett.contrast)
postell.vs.burnett.ebayes <- eBayes(postell.vs.burnett.fit)
#postell.vs.new.market
postell.vs.new.market.contrast <-
makeContrasts(postell-new.market,levels=
site.design)
postell.vs.new.market.fit <- contrasts.fit(oyster.site.lm,
postell.vs.new.market.contrast)
postell.vs.new.market.ebayes <- eBayes(postell.vs.new.market.fit)
#postell.vs.hewletts
postell.vs.hewletts.contrast <- makeContrasts(postell-hewletts,levels=
site.design)
postell.vs.hewletts.fit <- contrasts.fit(oyster.site.lm,
postell.vs.hewletts.contrast)
postell.vs.hewletts.ebayes <- eBayes(postell.vs.hewletts.fit)
#postell.vs.masonboro
postell.vs.masonboro.contrast <- makeContrasts(postell-
masonboro,levels=
site.design)
postell.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
postell.vs.masonboro.contrast)
postell.vs.masonboro.ebayes <- eBayes(postell.vs.masonboro.fit)
#postell.vs.whiskey
postell.vs.whiskey.contrast <- makeContrasts(postell-whiskey,levels=
site.design)
postell.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
postell.vs.whiskey.contrast)
postell.vs.whiskey.ebayes <- eBayes(postell.vs.whiskey.fit)
#postell.vs.james.island
postell.vs.james.island.contrast <- makeContrasts(postell-james.island
,levels=site.design)
postell.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
postell.vs.james.island.contrast)
postell.vs.james.island.ebayes <- eBayes(postell.vs.james.island.fit)
#burnett.vs.new.market
burnett.vs.new.market.contrast <-
makeContrasts(burnett-new.market,levels=
site.design)
burnett.vs.new.market.fit <- contrasts.fit(oyster.site.lm,
burnett.vs.new.market.contrast)
burnett.vs.new.market.ebayes <- eBayes(burnett.vs.new.market.fit)
#burnett.vs.hewletts
burnett.vs.hewletts.contrast <- makeContrasts(burnett-hewletts,levels=
site.design)
burnett.vs.hewletts.fit <- contrasts.fit(oyster.site.lm,
burnett.vs.hewletts.contrast)
burnett.vs.hewletts.ebayes <- eBayes(burnett.vs.hewletts.fit)
#burnett.vs.masonboro
burnett.vs.masonboro.contrast <- makeContrasts(burnett-
masonboro,levels=
site.design)
burnett.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
burnett.vs.masonboro.contrast)
burnett.vs.masonboro.ebayes <- eBayes(burnett.vs.masonboro.fit)
#burnett.vs.whiskey
burnett.vs.whiskey.contrast <- makeContrasts(burnett-whiskey,levels=
site.design)
burnett.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
burnett.vs.whiskey.contrast)
burnett.vs.whiskey.ebayes <- eBayes(burnett.vs.whiskey.fit)
#burnett.vs.james.island
burnett.vs.james.island.contrast <- makeContrasts(burnett-james.island
,levels=site.design)
burnett.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
burnett.vs.james.island.contrast)
burnett.vs.james.island.ebayes <- eBayes(burnett.vs.james.island.fit)
#new.market.vs.hewletts
new.market.vs.hewletts.contrast <-
makeContrasts(new.market-hewletts,levels=
site.design)
new.market.vs.hewletts.fit <- contrasts.fit(oyster.site.lm,
new.market.vs.hewletts.contrast)
new.market.vs.hewletts.ebayes <- eBayes(new.market.vs.hewletts.fit)
#new.market.vs.masonboro
new.market.vs.masonboro.contrast <- makeContrasts(new.market-masonboro
,levels=site.design)
new.market.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
new.market.vs.masonboro.contrast)
new.market.vs.masonboro.ebayes <- eBayes(new.market.vs.masonboro.fit)
#new.market.vs.whiskey
new.market.vs.whiskey.contrast <-
makeContrasts(new.market-whiskey,levels=
site.design)
new.market.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
new.market.vs.whiskey.contrast)
new.market.vs.whiskey.ebayes <- eBayes(new.market.vs.whiskey.fit)
#new.market.vs.james.island
new.market.vs.james.island.contrast <-
makeContrasts(new.market-james.island
,levels=site.design)
new.market.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
new.market.vs.james.island.contrast)
new.market.vs.james.island.ebayes <-
eBayes(new.market.vs.james.island.fit)
#hewletts.vs.masonboro
hewletts.vs.masonboro.contrast <-
makeContrasts(hewletts-masonboro,levels=
site.design)
hewletts.vs.masonboro.fit <- contrasts.fit(oyster.site.lm,
hewletts.vs.masonboro.contrast)
hewletts.vs.masonboro.ebayes <- eBayes(hewletts.vs.masonboro.fit)
#hewletts.vs.whiskey
hewletts.vs.whiskey.contrast <- makeContrasts(hewletts-whiskey,levels=
site.design)
hewletts.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
hewletts.vs.whiskey.contrast)
hewletts.vs.whiskey.ebayes <- eBayes(hewletts.vs.whiskey.fit)
#hewletts.vs.james.island
hewletts.vs.james.island.contrast <- makeContrasts(hewletts-
james.island
,levels=site.design)
hewletts.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
hewletts.vs.james.island.contrast)
hewletts.vs.james.island.ebayes <-
eBayes(hewletts.vs.james.island.fit)
#masonboro.vs.whiskey
masonboro.vs.whiskey.contrast <- makeContrasts(masonboro-
whiskey,levels=
site.design)
masonboro.vs.whiskey.fit <- contrasts.fit(oyster.site.lm,
masonboro.vs.whiskey.contrast)
masonboro.vs.whiskey.ebayes <- eBayes(masonboro.vs.whiskey.fit)
#masonboro.vs.james.island
masonboro.vs.james.island.contrast <-
makeContrasts(masonboro-james.island
,levels=site.design)
masonboro.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
masonboro.vs.james.island.contrast)
masonboro.vs.james.island.ebayes <-
eBayes(masonboro.vs.james.island.fit)
#whiskey.vs.james.island
whiskey.vs.james.island.contrast <- makeContrasts(whiskey-james.island
,levels=site.design)
whiskey.vs.james.island.fit <- contrasts.fit(oyster.site.lm,
whiskey.vs.james.island.contrast)
whiskey.vs.james.island.ebayes <- eBayes(whiskey.vs.james.island.fit)
site.tests <- list(decideTests(guerin.vs.village.ebayes,lfc=0),
decideTests(guerin.vs.duplin.ebayes,lfc=0),
decideTests(guerin.vs.oakdale.ebayes,lfc=0),
decideTests(guerin.vs.postell.ebayes,lfc=0),
decideTests(guerin.vs.burnett.ebayes,lfc=0),
decideTests(guerin.vs.new.market.ebayes,lfc=0),
decideTests(guerin.vs.hewletts.ebayes,lfc=0),
decideTests(guerin.vs.masonboro.ebayes,lfc=0),
decideTests(guerin.vs.whiskey.ebayes,lfc=0),
decideTests(guerin.vs.james.island.ebayes,lfc=0),
decideTests(village.vs.duplin.ebayes,lfc=0),
decideTests(village.vs.oakdale.ebayes,lfc=0),
decideTests(village.vs.postell.ebayes,lfc=0),
decideTests(village.vs.burnett.ebayes,lfc=0),
decideTests(village.vs.new.market.ebayes,lfc=0),
decideTests(village.vs.hewletts.ebayes,lfc=0),
decideTests(village.vs.masonboro.ebayes,lfc=0),
decideTests(village.vs.whiskey.ebayes,lfc=0),
decideTests(village.vs.james.island.ebayes,lfc=0),
decideTests(duplin.vs.oakdale.ebayes,lfc=0),
decideTests(duplin.vs.postell.ebayes,lfc=0),
decideTests(duplin.vs.burnett.ebayes,lfc=0),
decideTests(duplin.vs.new.market.ebayes,lfc=0),
decideTests(duplin.vs.hewletts.ebayes,lfc=0),
decideTests(duplin.vs.masonboro.ebayes,lfc=0),
decideTests(duplin.vs.whiskey.ebayes,lfc=0),
decideTests(duplin.vs.james.island.ebayes,lfc=0),
decideTests(oakdale.vs.postell.ebayes,lfc=0),
decideTests(oakdale.vs.burnett.ebayes,lfc=0),
decideTests(oakdale.vs.new.market.ebayes,lfc=0),
decideTests(oakdale.vs.hewletts.ebayes,lfc=0),
decideTests(oakdale.vs.masonboro.ebayes,lfc=0),
decideTests(oakdale.vs.whiskey.ebayes,lfc=0),
decideTests(oakdale.vs.james.island.ebayes,lfc=0),
decideTests(postell.vs.burnett.ebayes,lfc=0),
decideTests(postell.vs.new.market.ebayes,lfc=0),
decideTests(postell.vs.hewletts.ebayes,lfc=0),
decideTests(postell.vs.masonboro.ebayes,lfc=0),
decideTests(postell.vs.whiskey.ebayes,lfc=0),
decideTests(postell.vs.james.island.ebayes,lfc=0),
decideTests(burnett.vs.new.market.ebayes,lfc=0),
decideTests(burnett.vs.hewletts.ebayes,lfc=0),
decideTests(burnett.vs.masonboro.ebayes,lfc=0),
decideTests(burnett.vs.whiskey.ebayes,lfc=0),
decideTests(burnett.vs.james.island.ebayes,lfc=0),
decideTests(new.market.vs.hewletts.ebayes,lfc=0),
decideTests(new.market.vs.masonboro.ebayes,lfc=0),
decideTests(new.market.vs.whiskey.ebayes,lfc=0),
decideTests(new.market.vs.james.island.ebayes,lfc=0),
decideTests(hewletts.vs.masonboro.ebayes,lfc=0),
decideTests(hewletts.vs.whiskey.ebayes,lfc=0),
decideTests(hewletts.vs.james.island.ebayes,lfc=0),
decideTests(masonboro.vs.whiskey.ebayes,lfc=0),
decideTests(masonboro.vs.james.island.ebayes,lfc=0),
decideTests(whiskey.vs.james.island.ebayes,lfc=0))
names(site.tests) <- c(
"guerin.vs.village",
"guerin.vs.duplin",
"guerin.vs.oakdale",
"guerin.vs.postell",
"guerin.vs.burnett",
"guerin.vs.new.market",
"guerin.vs.hewletts",
"guerin.vs.masonboro",
"guerin.vs.whiskey",
"guerin.vs.james.island",
"village.vs.duplin",
"village.vs.oakdale",
"village.vs.postell",
"village.vs.burnett",
"village.vs.new.market",
"village.vs.hewletts",
"village.vs.masonboro",
"village.vs.whiskey",
"village.vs.james.island",
"duplin.vs.oakdale",
"duplin.vs.postell",
"duplin.vs.burnett",
"duplin.vs.new.market",
"duplin.vs.hewletts",
"duplin.vs.masonboro",
"duplin.vs.whiskey",
"duplin.vs.james.island",
"oakdale.vs.postell",
"oakdale.vs.burnett",
"oakdale.vs.new.market",
"oakdale.vs.hewletts",
"oakdale.vs.masonboro",
"oakdale.vs.whiskey",
"oakdale.vs.james.island",
"postell.vs.burnett",
"postell.vs.new.market",
"postell.vs.hewletts",
"postell.vs.masonboro",
"postell.vs.whiskey",
"postell.vs.james.island",
"burnett.vs.new.market",
"burnett.vs.hewletts",
"burnett.vs.masonboro",
"burnett.vs.whiskey",
"burnett.vs.james.island",
"new.market.vs.hewletts",
"new.market.vs.masonboro",
"new.market.vs.whiskey",
"new.market.vs.james.island",
"hewletts.vs.masonboro",
"hewletts.vs.whiskey",
"hewletts.vs.james.island",
"masonboro.vs.whiskey",
"masonboro.vs.james.island",
"whiskey.vs.james.island"
)
########## 1 ANOVA
all.sites.contrast <- makeContrasts(
guerin-village,
guerin-duplin,
guerin-oakdale,
guerin-postell,
guerin-burnett,
guerin-new.market,
guerin-hewletts,
guerin-masonboro,
guerin-whiskey,
guerin-james.island,
village-duplin,
village-oakdale,
village-postell,
village-burnett,
village-new.market,
village-hewletts,
village-masonboro,
village-whiskey,
village-james.island,
duplin-oakdale,
duplin-postell,
duplin-burnett,
duplin-new.market,
duplin-hewletts,
duplin-masonboro,
duplin-whiskey,
duplin-james.island,
oakdale-postell,
oakdale-burnett,
oakdale-new.market,
oakdale-hewletts,
oakdale-masonboro,
oakdale-whiskey,
oakdale-james.island,
postell-burnett,
postell-new.market,
postell-hewletts,
postell-masonboro,
postell-whiskey,
postell-james.island,
burnett-new.market,
burnett-hewletts,
burnett-masonboro,
burnett-whiskey,
burnett-james.island,
new.market-hewletts,
new.market-masonboro,
new.market-whiskey,
new.market-james.island,
hewletts-masonboro,
hewletts-whiskey,
hewletts-james.island,
masonboro-whiskey,
masonboro-james.island,
whiskey-james.island,
levels=site.design)
all.sites.fit <- contrasts.fit(oyster.site.lm,all.sites.contrast)
all.sites.ebayes <- eBayes(all.sites.fit)
all.sites.result <- decideTests(all.sites.ebayes,lfc=0)
> for(a in 1:dim(all.sites.result)[2])
+ print(sum(all.sites.result[,a]==site.tests[[a]]))
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
[1] 5440
> sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets"
"methods"
[7] "base"
other attached packages:
limma
"2.10.5"
On 9/12/07, Stephen Henderson <s.henderson at="" ucl.ac.uk=""> wrote:
>
> why not?
>
> ... the usual and then
> con.matrix<- matrix( -1/69, 70, 70)
> for (i in 1:70){ cm[i,i]<-1}
>
> colnames (con.matrix)<- levels (myClasses)
>
> fit2<- contrasts.fit (fit1, con.matrix)
> fit2<-eBayes(fit2)
>
> topTable (fit2, coef=65, genelist=whatever)
>
>
>
> ________________________________
>
> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Lana
Schaffer
> Sent: Tue 11/09/2007 22:46
> To: Naomi Altman; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] analysis of 70 groups for differential
expression
>
>
>
> Naomi,
> Yes, you are correct.
> Lana
>
> -----Original Message-----
> From: Naomi Altman [mailto:naomi at stat.psu.edu]
> Sent: Tuesday, September 11, 2007 2:19 PM
> To: Lana Schaffer; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] analysis of 70 groups for differential
expression
>
> If I understand you correctly, this is one-way ANOVA with 69
contrasts,
> not 69 separate ANOVAs (or t-tests). I.e. 1 run of limma with a
huge
> contrast matrix.
>
> --Naomi
>
> At 12:14 PM 9/11/2007, Lana Schaffer wrote:
>
> >Hi,
> >We have a situation were there are 70 groups and we want to know if
> >there is differential expression in a group. I think of the
problem
as
>
> >contrasting the expression of 1 group and the rest of the groups.
> >In this case, limma would need to done 70 times for each group
contrast
>
> >versis the rest of the groups.
> >But this would result in an uneven comparison between one group and
70
> >other groups. Can someone suggest a way to approach this problem?
> >
> >Lana Schaffer
> >Biostatistics/Informatics
> >The Scripps Research Institute
> >DNA Array Core Facility
> >La Jolla, CA 92037
> >(858) 784-2263
> >(858) 784-2994
> >schaffer at scripps.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
>
> Naomi S. Altman 814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics 814-863-7114 (fax)
> Penn State University 814-865-1348
(Statistics)
> University Park, PA 16802-2111
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
>
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>
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>
>
>
>
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>
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