[BioC] how to transform all data into log(base 2) values

Ting-Yuan Liu (FHCRC) tliu at fhcrc.org
Wed Jul 20 09:02:11 CEST 2005

Hi Weinong,

What kind of format your data is?  If you can read the data into Excel, 
you can save the Excel file as *.csv.  Then use the function "read.csv" in 
R to read the csv file.  In R, you can very easy to transform the 
expression values by log2(array1), log2(array2), etc.  After the 
transformation, write the object to be a csv file again (by write.table) 
or other format you prefer.  Does it make sense?


PS.  You may find the R function apply() useful.  

On Tue, 19 Jul 2005, weinong han wrote:

> Hi, All,
> I want to transform Affymetrix MAS expression values (above 20,000) into log(base 2) values with header(arry1, array2, array3...) and gene names(gene1, gene2, gene3...) intact. Transformation of log(base 2) one column one time in Excel is laborious, albeit well done.
> Anyone have the experience?
> Any advice and suggestions will be much appreciated.
> Many thanks in adavance.
> l
> Best Regards
> Han Weinong  
> hanweinong at yahoo.com
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