[BioC] limma2annaffy error

[James W. MacDonald]

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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
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