Hi,
I have two data set of normalized Affymetrix CEL files, wild type vs Control
type.(each set have further three replicates).
> 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"
So, how to troubleshoot this problem?
Regards,
Sukhbir Singh Rattan.....
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