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Batch effect adjustment using Housekeeping Genes

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.

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Re: Batch effect adjustment using Housekeeping Genes

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

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com