[BioC] ReportingTools error

[James W. MacDonald]

Hi Jason,

I see the same thing - I had an email exchange with Gordon back in 
February and he agreed that the row.names of the output from topTable 
and topTableF should be the same thing, and it looked like he was 
leaning towards using the row numbers. Given the speed with which he 
updates things in limma, I assumed this happened approximately 13 
nanoseconds later, but evidently it either fell through the cracks or he 
had a change of mind (Gordon is cc'ed).

But I wonder if the ID column is a better way to go anyway.

Gordon - what is the safest way to use data from either topTable or 
topTableF to extract the corresponding raw data from the input object? 
Is the ID column guaranteed to always correspond to the row.names or 
featureNames of the data passed into lmFit?

Best,

Jim

 > sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
  [1] ReportingTools_2.1.2      knitr_1.2
  [3] lattice_0.20-15           affycoretools_1.32.0
  [5] KEGG.db_2.9.0             GO.db_2.9.0
  [7] AnnotationDbi_1.22.1      affy_1.38.0
  [9] pd.ragene.1.0.st.v1_3.8.0 RSQLite_0.11.2
[11] DBI_0.2-5                 limma_3.16.1
[13] oligo_1.24.0              Biobase_2.20.0
[15] oligoClasses_1.22.0       BiocGenerics_0.6.0

[snip]



On 4/11/2013 9:24 PM, Jason Hackney wrote:
> 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 at uw.edu 
> <mailto:jmacdon at 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 at gene.com <mailto:hackney.jason at gene.com>
> 650-467-5084
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099