HI,
I need some suggestion regarding Differentially expressed genes. I have a condition where I donot have any statistically significant differentially expressed genes from my cuffdiff output for the gene_exp.diff file. And also the q value is not significant as well. Only the original p values are significant and the fold change can be considered for up regulation and dow regulation comparison. I would like to know in this scenario how shall I select the genes of interest for Gene ontology analysis. And what criteria should I choose to filter out the up regulated and down regulated genes in the comparison. It would be good if someone provides me with suggestions.
I need some suggestion regarding Differentially expressed genes. I have a condition where I donot have any statistically significant differentially expressed genes from my cuffdiff output for the gene_exp.diff file. And also the q value is not significant as well. Only the original p values are significant and the fold change can be considered for up regulation and dow regulation comparison. I would like to know in this scenario how shall I select the genes of interest for Gene ontology analysis. And what criteria should I choose to filter out the up regulated and down regulated genes in the comparison. It would be good if someone provides me with suggestions.
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