Thanks a lot Jim, it was really helpful!!!
I debugged the function and found the problem.
My lmFit object, and hence the "tables" object contain gene symbols which I
added to the lmFit object in some point. In the code when it reaches the
line "aafTable(`Fold Change` = round(fld, 2))" it actually reads the symbols
instead of the fold change.
May I suggest to replace the line "fld<-tables[[i]][,2]" with
"fld<-tables[[i]][,"logFC"], this can prevent the error in the future.

I solved this problem and encountered another one, and after debugging I
think I found a small bug in the code.
The problem appears when I set in the command line "tstat = FALSE". The
first hrml file for the first contrast is generated successfully, but when
it comes to generate the "testtable" for the second contrast I get the error


"Error in merge.aafTable(testtable, aafTable(`p-value` =
round(tables[[i]][,  :
  The tables must have the same number of rows"

This is because when tstat=FALSE, the testtable is not reset and updated to
the new comparison.

 >if (tstat) testtable <- aafTable(`t-statistic` = round(tables[[i]][, "t"],
2))
 >if (pval) {
 >   if (!exists("testtable")) {
 >      testtable <- aafTable(`p-value` = round(tables[[i]][,
 >           "adj.P.Val"], 3))
 >   }
 >   else {
 >       testtable <- merge(testtable, aafTable(`p-value` =
round(tables[[i]][,
 >           "adj.P.Val"], 3)))
 >   }
>}

When I set "tstat=TRUE"  everything is OK

All the best
Mali







This
All the best
Mali

On Wed, Mar 16, 2011 at 3:32 PM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> Hi Mali,
>
>
> On 3/16/2011 3:23 AM, mali salmon wrote:
>
>> Hi All
>> I am analysing affymetrix data, and I am trying to use "limma2annaffy"
>> function from "affycoretools" package to create html tables.
>> When I run the following command:
>>
>>  limma2annaffy(eset, fit2, design, cont.matrix,lib="hgu133a2" , adjust =
>>>
>> "fdr",
>>       anncols = aaf.handler()[c(1:3, 4:5, 11:12)], pfilt =
>> 0.05,fldfilt=2,tstat = FALSE, pval = TRUE, FC = TRUE,
>>       expression = TRUE, html = TRUE, text = FALSE, save = FALSE)
>> I get the error:
>> "Error in round(fld, 2) : Non-numeric argument to mathematical function"
>>
>> In order to understand why I get this error, I have tried to generate the
>> "tables" object from the limma2annaffy code.
>> However, when I get to "tableFilt" function, R can't find it although the
>> package is loaded.
>>
>
> The easiest way to debug a function is to do
>
> debug(limma2annaffy)
>
> then run the function call. You can then step through the execution of the
> function line by line, and look at the intermediate objects being made, such
> as the tables list. Since you will be debugging from within the package
> namespace, all functions will be available to you.
>
> Note however that the tableFilt() function simply takes the output from
> topTable() and then filters based on the p-value and fold change you
> supplied. The error indicates that you are getting non-numeric values in the
> second column of your topTable() output, which is unexpected.
>
>
>
>> When I type ?tableFilt I get the documentation, but when I try to view the
>> code I get
>>
>>> tableFilt
>>>
>> Error: object 'tableFilt' not found
>>
>
> That's because this package has a namespace, and the tableFilt() function
> isn't exported. You can access unexported functions using :::, e.g.,
> affycoretools:::tableFilt.
>
> Best,
>
> Jim
>
>
>
>> Any ideas?
>> Thanks
>> Mali
>>
>>
>>  sessionInfo()
>>>
>> R version 2.12.1 (2010-12-16)
>> Platform: i386-redhat-linux-gnu (32-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=C              LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] hgu133a2.db_2.4.5    org.Hs.eg.db_2.4.6   annaffy_1.22.0
>>  [4] annotate_1.28.0      affycoretools_1.22.0 KEGG.db_2.4.5
>>  [7] GO.db_2.4.5          RSQLite_0.9-4        DBI_0.2-5
>> [10] AnnotationDbi_1.12.0 simpleaffy_2.26.1    gcrma_2.22.0
>> [13] genefilter_1.32.0    hgu133a2cdf_2.7.0    affy_1.28.0
>> [16] Biobase_2.10.0       limma_3.6.9
>>
>> loaded via a namespace (and not attached):
>>  [1] affyio_1.18.0         biomaRt_2.6.0         Biostrings_2.18.2
>>  [4] Category_2.16.1       GOstats_2.16.0        graph_1.28.0
>>  [7] GSEABase_1.12.2       IRanges_1.8.9         preprocessCore_1.12.0
>> [10] RBGL_1.26.0           RCurl_1.5-0           splines_2.12.1
>> [13] survival_2.36-2       tcltk_2.12.1          tools_2.12.1
>> [16] XML_3.2-0             xtable_1.5-6
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>

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