[Bioc-devel] lumi data import bug

[Martin Morgan]

Florian, Pan -- earlier in lumiR (I guess this is where the problem
is?) read.table can have an argument 'dec'. This might be exposed as
an explicit argument, or, lumiR could have a ... and pass that to
read.table.

Martin

Florian Hahne <f.hahne at dkfz-heidelberg.de> writes:

> Hi Pan Du,
> I just tried to import some of my Illumina data using you nice lumi 
> package. However, lumiR stopped with an error message. When debugging 
> the function I noticed that the problem is in the decimal separator that 
> is used for numeric data. For the output on a German PC BeadStudio uses 
> commas as decimal separators (which is for some strange historic reason 
> the German convention...). Now the following will produce a matrix of 
> NAs since R doesn't know how to convert e.g. 1,2312 to a numeric
>  if (!is.numeric(exprs[1])) {
>             exprs <- matrix(as.numeric(exprs), nrow = nrow(allData))
>         }
>
> My rather naiv approach of fixing this is to include the following:
> if (!is.numeric(exprs[1])) {
>     exprs <- gsub(",", ".", exprs, fixed=TRUE)
>     exprs <- matrix(as.numeric(exprs), nrow = nrow(allData))
>         }
>
> Of course the same needs to be done for the other numeric columns as 
> well. There might be a more elegant way to figure out the separator and 
> fix this already before.
>
> Hope this helps in your development process,
> Florian
>
>
>
>
>  > sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-06-11 r41910)
> i686-pc-linux-gnu
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
> attached base packages:
> [1] tcltk     tools     stats     graphics  grDevices datasets  utils   
> [8] methods   base    
> other attached packages:
>  [1] debug_1.1.0           mvbutils_1.1.1        lumi_1.3.13         
>  [4] annotate_1.15.2       AnnotationDbi_0.0.78  RSQLite_0.5-4       
>  [7] DBI_0.2-3             mgcv_1.3-24           affy_1.15.7         
> [10] preprocessCore_0.99.7 affyio_1.5.4          Biobase_1.15.14     
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-13
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org