[BioC] Error: couldn't find function "-<-"

[S Peri]

Hello Dr. Ramasamy,
Thank you for your mail. I loaded only 49 files
instead of 50. 
 
 I am writing the a function for T-test and the
following error creeps in always.

Could you pls. let me know if the problem is in
defining function or something else. 
Thank you.

PS


> T-test <- function(X,CL){
+ ttest <- function(Xrow,CL){
+ return(t.test(Xrow[CL==0],Xrow[CL==1])$p.value)
+ }
+ return(apply(X,1,ttest,CL=CL))
+ }
Error: couldn't find function "-<-"









--- Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
wrote:

> First thing first. Are you sure justRMA is returning
> expression for 49
> arrays when you have 50 files in the working
> directory ?
> 
> getwd()
> library(affy)
> length(list.celfiles())
> 
> If you accidentally deleted one CEL file, this could
> be the reason later
> calls also fail.
> 
> 
> On Tue, 2004-08-17 at 17:44, S Peri wrote:
> > Dear Group, 
> >  
> > I am analyzing Affy dataset from Harvard Brain CEL
> > database. 
> > 
> > I am working on the data from an experiment where
> 50
> > samples were analyzed.  I exported the expressions
> to
> > a matrix. 
> > 
> > >gliexp <- exprs(justRMA())
> > > dim(gliexp)
> > [1] 12625    49
> > 
> > 
> > I sorted out samples on the pathological state (4
> > categories).  Now I want to do SAM and t-test on
> any
> > of the 2 samples. 
> > 
> > I made these 4 categories into 0,1,2 and 3. This
> was
> > made in a class file : Brain.cl
> > 
> > I wrote a function where values from 0 and 1 will
> give
> > me the means from 0 and 1.
> > 
> > My function:
> > 
> > >BrainFc <- function(exp,cl){
> > +X0 = X[,cl==0]
> > +X1 = X[,cl==1]
> > +return(apply(X0,1,mean) - apply(X1,1,mean))}
> > 
> > >myBrainFcs <- BrainFc(gliexp,Brain.cl)
> > Error in X[, CL == 0] : incorrect number of
> dimensions
> > 
> > 
> > I do not understand why am I getting this error.
> > 
> > I checked to see dim of my expression matrix:
> > > dim(gliexp)
> > [1] 12625    49
> > 
> > I have 50 samples, here I see 49.
> > 
> > Is this is the source of error? If so what should
> I
> > do?
> > 
> > 
> > I also did the following by reading previous
> messages
> > from BioC mailing lists:
> > 
> > > gliexp_genes <- gliexp[1:12625,]
> > > myBrainFcs <- BrainFc(gliexp_genes,Brain.cl)
> > 
> > Error in BrainFc(gliexp_genes, Brain.cl) :
> (subscript)
> > logical subscript too long
> > 
> > 
> > After this I do not have any option to write to
> BioC
> > for some help. 
> > 
> > Please help me where I am doing wrong.
> > 
> > Thank you
> > 
> > PS
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
>