[BioC] Differentially expressed gene list

[James MacDonald]

Hi Sara,

There are several problems here. First, you are computing fold change as if the data are log2 transformed, but then you are selecting genes based on fold change as if the data are not logged. If I assume you want two-fold differentially expressed genes, the down-regulated genes will have fold differences of -1 or less, not less than 1.

Second, you are taking absolute value in your 'fold' function, so you won't find any down-regulated genes anyway (this is likely the source of your warning message).

Third, there are much more efficient ways to compute the fold change than the way you are doing it. You could do it in one line, without even having to write a function.


fold <- rowMeans(Data[,1:5]) - rowMeans(Data[,6:10])

Best,

Jim




>>> <carotenuto at igb.cnr.it> 10/07/05 10:11 AM >>>


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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