Dear experts,
I just started working in the field of RNA sequencing and would be very grateful to get an advice from you.
I started with a set of two patients and two wild types in the hope of identifying a gene, which is not expressed in the patients. I used the pipeline and recipe of the genepattern workspace (http://recipes.genomespace.org/view/6) and I finally get a list with the FPKMs of the four different samples. There were two genes, which were virtually not expressed in both patients (FPKM = 0) while both wild types showed high expression (gene 1: FPKM > 8000; gene 2: > 3000). The status was marked as "High Data". Moreover, no errors occured during the execution. The problem is now, that these two genes were actually expressed in the patients (verified by qRT-PCR, mass spec and western blotting). So, do you have any idea, how this false result emerges?
Thanks a lot!
I just started working in the field of RNA sequencing and would be very grateful to get an advice from you.
I started with a set of two patients and two wild types in the hope of identifying a gene, which is not expressed in the patients. I used the pipeline and recipe of the genepattern workspace (http://recipes.genomespace.org/view/6) and I finally get a list with the FPKMs of the four different samples. There were two genes, which were virtually not expressed in both patients (FPKM = 0) while both wild types showed high expression (gene 1: FPKM > 8000; gene 2: > 3000). The status was marked as "High Data". Moreover, no errors occured during the execution. The problem is now, that these two genes were actually expressed in the patients (verified by qRT-PCR, mass spec and western blotting). So, do you have any idea, how this false result emerges?
Thanks a lot!
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