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R package to find differentialy expressed genes

Hello, I have three groups of samples, each with 10 values. Each group represent HIV-1 stage.I have 124 genes and I want to find differentially expressed genes across these three groups. I tried for two groups of samples using rowMeans(). Please help me .

sample of my query is given below:

    s1 s1 s1 s1 s1 s1 s1 s1 s1 s1 |   s2 s2 s2  s2 s2 s2  s2 s2 s2 s2 |  s3 s3 s3 s3  s3 s3 s3 s3 s3 s3
g1                                |                                                 |
g2                                |                                                 |
g3                                |                                                 |
g4                                |                                                 |
-                                 |                                                |
-                                 |                                                |
-                                 |                                                |
g124                              |                                                |
r gene
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updated by Nicolas Rosewick Nicolas Rosewick • written by tulika.kakati • tulika.kakati

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written by WouterDeCoster WouterDeCoster

How did you generate this data? qPCR? RNA-seq?

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written by WouterDeCoster WouterDeCoster

1 answer

Use limma, DESeq2 or edgeR. Search in biostars you'll find a lot of similar questions.

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written by Nicolas Rosewick Nicolas Rosewick

He writes he has 124 genes so I'm not sure he has RNA-seq data...

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written by WouterDeCoster WouterDeCoster

True, but I doubt whether the models of DESeq2 etc with regard to dispersion estimation still stand with such a limited number of genes.

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written by WouterDeCoster WouterDeCoster

I've seen DESeq2 used for miRNA where you only have a few hundred "genes", so it's not entirely unreasonable.

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written by igor igor

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