[BioC] Fold change GEO data

[Sean Davis]

On Tue, Sep 9, 2008 at 1:31 PM, hemant ritturaj
<ritturajhemant at gmail.com> wrote:
> Dear Sean,
>
> My apologies for the errror.
>
> Here I am giving the complete error which i am getting
>
>> gse <- getGEO('gse6901')[[1]]
>> exprs(gse)
>> log2(exprs(gse))
>> set <- log2(exprs(gse))
>> targets <- c('A','A','A','B','B','B','C','C','C','D','D','D')
>> f <- factor(targets,levels=c('A','B','C','D'))
>> design <- model.matrix(~0+f)
>> contrast.matrix <- makeContrasts(fA-fB,fA-fC,fA-fD,levels=design)
>> fit <- lmFit(set,design,method="robust")
>> fit2 <- contrasts.fit(fit,contrast.matrix)
>> fit2 <- ebayes(fit2)
>
>> names(fit2)
> [1] "df.prior"  "s2.prior"  "s2.post"   "t"         "p.value"   "var.prior"
> [7] "lods"
>
> topTable(fit2,n=10)
> Error in if (ncol(fit) > 1) return(topTableF(fit, number = number, genelist
> = genelist,  :
>  argument is of length zero

This works for me:

gse <- getGEO('gse6901')[[1]]
exprs(gse) <- log2(exprs(gse)+1) # avoid log2(0) since we are not normalizing
targets <- c('A','A','A','B','B','B','C','C','C','D','D','D')
f <- factor(targets,levels=c('A','B','C','D'))
design <- model.matrix(~0+f)
contrast.matrix <- makeContrasts(fA-fB,fA-fC,fA-fD,levels=design)
fit <- lmFit(gse,design) # you can use an ExpressionSet just fine in limma
fit2 <- contrasts.fit(fit,contrast.matrix)
fit2 <- eBayes(fit2)
names(fit2)

 [1] "coefficients"     "rank"             "assign"           "qr"
 [5] "df.residual"      "sigma"            "cov.coefficients" "stdev.unscaled"
 [9] "genes"            "Amean"            "method"           "design"
[13] "contrasts"        "df.prior"         "s2.prior"         "var.prior"
[17] "proportion"       "s2.post"          "t"                "p.value"
[21] "lods"             "F"                "F.p.value"

Again, start with a clean workspace, load GEOquery and limma, then
paste the above commands into the window.  Let us know if you have
further questions.