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. So, how to troubleshoot this problem? Regards, Sukhbir Singh Rattan..... [[alternative HTML version deleted]]

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 [[alternative HTML version deleted]]