[R] Differentially expressed gene list

From: <carotenuto_at_igb.cnr.it>
Date: Sat 08 Oct 2005 - 00:36:49 EST

Hi,when I perform SAM on my array data(siggenes)I have some problems in retrieving the separate lists of up regulated and down regulated genes. When I write:
fold<-function(x){ gruppi<-split(x,controllo)
geni1<-abs(mean(gruppi[[2]])-mean(gruppi[[1]])) return(geni1)
}
fold<-esApply(expr.contr.tratt.4,1,fold) filtro.geni.4_prova<-expr.contr.tratt.4[which(fold>=1),] filtro.geni.4_prova

everything is working well and I can obtain the correct HTML output,but if I write the same using fold change<1 to obtain downregulated genes,I have the following warning message:

###Warning messages:
####1: the condition has length > 1 and only the first element will be used in:
if (!nchar(text <- getText(object))) return("")
####2: the condition has length > 1 and only the first element will be used in:
if (!nchar(text <- getText(object))) return("")
####3: the condition has length > 1 and only the first element will be used in:
if (!nchar(text <- getText(object))) return("")
####4: the condition has length > 1 and only the first element will be used in:
if (!nchar(text <- getText(object))) return("")
####5: the condition has length > 1 and only the first element will be used in:
if (!nchar(text <- getText(object))) return("")

Where is the mistake?
Thank you for your help
Sara



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