Hi,
I am running edgeR and used plotSmear to visualize my results. When coloring only the genes that are DE by FDR<0.05 I see that many genes have a higher fold change than some of the DE genes and that some of the DE genes have a low fold change. This is only the case when I use estimateGLMTagwiseDisp and not when I use estimateGLMCommonDisp. Does this mean that using common dispersion is the best? I only have cases and controls in my data so I guess it should be good enough but I always thought estimating tagwise dispersion was better?
Also:
It also seems like ~90 % of my genes are up-regulated. I tried all the different normalization options but the results seem to be the same. Can this be true or could something be wrong with my data? Any way of testing that?
I am running edgeR and used plotSmear to visualize my results. When coloring only the genes that are DE by FDR<0.05 I see that many genes have a higher fold change than some of the DE genes and that some of the DE genes have a low fold change. This is only the case when I use estimateGLMTagwiseDisp and not when I use estimateGLMCommonDisp. Does this mean that using common dispersion is the best? I only have cases and controls in my data so I guess it should be good enough but I always thought estimating tagwise dispersion was better?
Also:
It also seems like ~90 % of my genes are up-regulated. I tried all the different normalization options but the results seem to be the same. Can this be true or could something be wrong with my data? Any way of testing that?
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