Batch effect adjustment using Housekeeping Genes

[#1]

Hello, starting from a txt file with count data, I am analysing RNAseq data from three different independent  experiments which should be merged into a single analysis. Sample characteristics, such as disease conditions, are perfectly confounded within the batches. The use of housekeeping genes, such as those suggested by Eisenberg et al. (http://dx.doi.org/10.1016/j.tig.2013.05.010), could be one way of addressing the batch effects. Is there a way in JMP Genomics which allows specifying sets of genes which could be used to adjust the batches?

Thank you so much for your time.

[#2]

Hi,

In JMP Genomics, you can use Loess Normalization within Expression>Normalization to specify a control set or housekeeping set of genes for normalization.  See documentation here:

http://www.jmp.com/support/downloads/JMPG90_documentation/wwhelp/wwhimpl/js/html/wwhelp.htm#href=PA_...

Hope this helps,

Chris