[BioC] Error with GAGE

[Martin Morgan]

On 01/27/2012 12:52 PM, Javerjung Sandhu wrote:
> Dear list,
>
> I am getting the error shown in red below:
>
>  > options(width=80)
>  > Micro_array_data <- data.matrix(readExpData(file =
> "Micro_array_dataset.txt"))

you are expecting a matrix with 6 columns, and with row names equal to 
gene symbols. Have you achieved this?

>  > Gene_set <- readList("c1_all_v3_0_symbols.gmt")
>  > A1_compare_un <- gage(exprs = Micro_array_data, gsets =
> Gene_set,set.size = c(10,50))

Your gene set includes genes that are not in your expression data, and 
your expression data has genes not in your gene sets. Make them consistent.

You specify a minimum gene set size of 10; do any of your gene sets, 
updated to contain only genes in your expression data, satisfy this?

Are the expression values measured on a scale (e.g., log) appropriate 
for gage?

gage expects more than one gene set.

> Error in if (is.na(spval[i])) tmp[i] <- NA : argument is of length zero
>  > class(Micro_array_data)
> [1] "matrix"
>  > dev.off()
> Error in dev.off() : cannot shut down device 1 (the null device)
>  > detach("package:gage")
>  >
>
> I have attached the input files used for this analysis. Help will be
> really appreciated.
>
> Thanks,
>
> Jung
>


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