[BioC] ComBat:RT-PCR Data

[Johnson, William Evan]

Hi Giuliano, 

ComBat should work fine, just be cautious about outlier genes and samples, because these could influence the results. Outliers are usually less of a problem in microarray studies because there are so many genes, but in your case outliers could have more influence. To check this, look for abnormalities in the heatmap and also look for gross violations from normality in the prior plots generated by ComBat.

Thanks!

Evan


On May 22, 2014, at 4:33 AM, Giuliano Stirparo <giulianostirparo at gmail.com> wrote:

>  Dear All
> I am trying to use combat to perform batch correction of RT-PCR data. In particular I have around 40 genes and 59 samples.
> The samples are divided in two categories (resistant on a particular treatment and sensitive) and they come from different batch (6 samples + 19 samples + 24 samples). 
> To perform batch correction I used the default parameter. I was wondering if it is possible use ComBat for this kind of analysis or if I have to try with different tools.
> If you need more details please do not hesitate to contact me.
> 
> Best 
> 
> Giuliano Stirparo