[BioC] ComBat

[W. Evan Johnson]

Gerhard, 

Thanks for the suggestion. I will definitely do this. I will also try to fix the column names bug in the ComBat.R script as well. I don't believe that the Bioconductor version of ComBat has problems with either of these bugs. 

Thanks!

Evan


On Nov 2, 2012, at 3:54 AM, Gerhard Thallinger wrote:

> Hi,
> 
>> 2. On line 3154, your gene description has some character formatting
>> that is causing issues with R's "read.table" function--which is used
>> by ComBat. I think its reading the apostrophe as quoted text, so it
>> is then concatenating everything after that as text until the next
>> apostrophe. 
>> Anyway, here is how you fix it: open up your dataset 
>> ('12arraysCombatImputed_2.txt') in Excel, then save it as a .csv. 
>> Then run ComBat using the option: type='csv'. 
>> Alternatively, you can remove the second column from your 
>> dataset for ComBat and then add them back in after adjustment.
> 
>  To make life easier for ComBat users and to avoid similar problems
>  in the future, quote="" should be added to the read.table() call
>  in ComBat.
> 
> Regards
> 
> Gerhard
> 
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> Dr. Gerhard Thallinger             E-mail:  Gerhard.Thallinger at tugraz.at
> Institute for Genomics and Bioinformatics   Web: http://genome.tugraz.at
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