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up regulated genes based on fold change

I have 50 different individuals in three biological replicates (50 x 3=150) Then I calculate the fold change using this 

sample/control 
replicate/control
replicate/ control

The second replicate is obtained in a shift time (I want to also get the idea on the time influence in my experiment) The third replicate is obtained in a bit more shift time

Now I would like to obtain which genes are up regulated and which one is down regulated.

My own idea is to sort the data based on the three expression. then select the top of the list as up and those that have a very low expression as down regulated. is it a good approach ?

gene
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updated by WouterDeCoster WouterDeCoster • written by Learner Learner

1 answer

I would suggest you have a look at the R/Bioconductor package limma: https://bioconductor.org/packages/release/bioc/html/limma.html

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written by WouterDeCoster WouterDeCoster

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