Understanding the concept of Up and down regulated genes

Question

[Learner]

I have been reading many comments related to how to find an unregulated or down regulated genes through a specific experimental data.

There are few posts which I found useful what is up and down regulated What Does Up-Regulated And Down-Regulated Mean？ and here Understanding up and down regulated genes from LOG2 foldchange or foldchange

This means we don't need to use any software to find out which gene is up or which genes is down regulated. If we have no replicated , we calculate Log fold change and those positive will be up and the negative will be down regulated. if we have replicated, we can perform ANOVA and see which one are different,

Sometimes we have expression which are not integers , so there I could not find a solution for it expect normalise the data

Is this a right conclusion ?

Answer 1

[WouterDeCoster]

You calculate a fold change based on just two samples, but this is meaningless since you'll not be able to see which genes are statistically significantly differentially expressed. Almost none of your genes will have the same level in two samples, does that mean that each gene is differentially expressed? Of course not.

Differential expression analysis is far more complicated than how you summarized it in your post.

[Learner]

@decosterwouter define statistically significantly different ! if you look inside , you can see that we can also assume a result based on one sample experiment . actually I suggest make an informative comment so other people and I can use it. You just read a part of my question and reply.

[WouterDeCoster]

Never mind then, good luck with your analysis.