[BioC] ComBat

[Gerhard Thallinger]

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

------------------------------------------------------------------------
Dr. Gerhard Thallinger             E-mail:  Gerhard.Thallinger at tugraz.at
Institute for Genomics and Bioinformatics   Web: http://genome.tugraz.at
Graz University of Technology               Tel:        +43 316 873 5343
Petersgasse 14/V                            Fax:      +43 316 873 105343
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