On Mon, Feb 28, 2011 at 1:02 AM, Sukhbir Rattan <sukhbir.rattan@gmail.com>wrote:

> Hi,
>
> I have two data set of normalized Affymetrix CEL files, wild type vs
> Control
> type.(each set have further three replicates).I have already done the
> normalization by using RMA function from affy package.
> Now, what I have is:
>
> > wild.fish
> AffyBatch object
> size of arrays=712x712 features (10 kb)
> cdf=Zebrafish (15617 affyids)
> number of samples=3
> number of genes=15617
> annotation=zebrafish
> notes=
> > Dicer.fish
> AffyBatch object
> size of arrays=712x712 features (10 kb)
> cdf=Zebrafish (15617 affyids)
> number of samples=3
> number of genes=15617
> annotation=zebrafish
> notes=
>
> Now, I have to combine these two S4 objects and use lmFit function of Limma
> package.I am able to combine the two S4 objects using merge function.
>
>
> > merge.fish <-merge(wild.fish,Dicer.fish)
> > merge.fish
> AffyBatch object
> size of arrays=712x712 features (17833 kb)
> cdf=Zebrafish (15617 affyids)
> number of samples=6
> number of genes=15617
> annotation=zebrafish
> notes=Merge from two AffyBatches with notes: 1)  , and 2)
>
> > design
>             Wild Mz_Dicer
> GSM95623.CEL    1        0
> GSM95624.CEL    1        0
> GSM95625.CEL    1        0
> GSM95617.CEL    0        1
> GSM95618.CEL    0        1
> GSM95619.CEL    0        1
>
>
> > fit <-lmFit(merge.fish, design)
> Error in as.vector(data) :
>  no method for coercing this S4 class to a vector
>
> > mode(merge.fish)
> [1] "S4"
>
> My problem is first, I have to do the normalization of CEL files
> differently(means wild type separately and dicer type differently),I can't
> do the normalization of all together, then there is merging problem and
> further ,whole protocol is effected.
>

Hi, Sukhbir.

You should probably do the normalization together.  Otherwise, your dicer/wt
fish will not be very comparable and it looks like you are comparing between
the two.

Sean

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