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.correlation
)


#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@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@stat.math.ethz.ch on behalf of Lana Schaffer
> Sent: Tue 11/09/2007 22:46
> To: Naomi Altman; bioconductor@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@stat.psu.edu]
> Sent: Tuesday, September 11, 2007 2:19 PM
> To: Lana Schaffer; bioconductor@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@scripps.edu
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor@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
>
> _______________________________________________
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>
>
>
> **********************************************************************
> This email and any files transmitted with it are confidentia...{{dropped}}
>
> _______________________________________________
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