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FKPM normalization: how to deal with cell type purity? vadoue Bioinformatics 0 11-19-2012 07:36 AM

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Old 11-19-2012, 07:38 AM   #1
Location: canada

Join Date: Nov 2010
Posts: 20
Default FKPM normalization: how to deal with cell type purity?

Hi all,
I hope that you can help me... I am working with some blood purified cells from different individuals and different time-points. My problem is that when I want to look at which genes are differentialy regulated in the same cell-type by between 2 time-points (6 month between the 2 blood donations) I found many genes differentially regulated but this seems to be due to cell purity: for example after monocytes purification the gene which represent the monocyte specificity CD14 is different (then we have some contamination by another cell type, even weak for highly expressed genes this make a difference) and for few genes I observed same ratio of variation between samples. Does anyone know how to deal with that ? I tried normalization of the data using limma and ggplot2 under R but it didn't work for that problem.
Thanks a lot for your help !!!
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