Hi Jim,

Could you send me your sessionInfo? I'm having trouble replicating this
bug. I'm still getting probe names for topTableF and row numbers for
topTable, as of limma_3.16.1. I'll pop in a bug fix to the ReportingTools
trunk tomorrow, once I get the limma version sorted.

Thanks,

Jason

On Thu, Apr 11, 2013 at 11:05 AM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi,
>
> I am getting an error when trying to create HTML pages with
> ReportingTools, using an MArrayLM object as input. The error I get is
>
> Error in expression.dat[probe, ] : subscript out of bounds
>
> which appears to come from .make.gene.plots(), specifically here:
>
>  for (probe in rownames(df)) {
>         if ("Symbol" %in% colnames(df)) {
>             ylab <- paste(df[probe, "Symbol"], ylab.type)
>         }
>         else {
>             ylab <- paste(probe, ylab.type)
>         }
>         bigplot <- stripplot(expression.dat[**probe, ] ~ factor,
>
> The problem being that the rownames for a topTable object will be the row
> numbers of the MArrayLM object from whence the data came (this was recently
> harmonized by Gordon Smyth, so the row.names will always be the row number,
> regardless of using topTable() or topTableF()).
>
> In other words, it appears that probe is assumed to be the row name, when
> in fact it will be the row number. So something like
>
> for(probe in as.numeric(rownames(df))){
>
> should do the trick.
>
> Best,
>
> Jim
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>


-- 
Jason A. Hackney, Ph.D.
Bioinformatics and Computational Biology
Genentech
hackney.jason@gene.com
650-467-5084

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