[BioC] ReportingTools error

[James W. MacDonald]

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