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RNA-Seq results comparison

Hi all,

I analyzed the fastq files (RNA-Seq) from an experiment where authors test two different treatments in E. coli. The dataset is comprised by nine files in total, 3 belong to the control, 3 to the treatment one and 3 to treatment two. Authors analyzed their data using DESeq2 and me using CLC Workbench. So there are differences in the obtained number of differentially expressed genes.

My question is: is there any statistical test I can apply to compare both results? The authors report the differentially expressed genes with their respective ratio and p-value.

rna-seq
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updated by dsull dsull • written by Spacebio Spacebio

1 answer

You could use a hypergeometric test if you just want to compare the two lists of genes.

You can also look at correlation between the p-values or correlation between the log2FC's from the two analyses.

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written by dsull dsull

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