Question: R package to find differentialy expressed genes
1
gravatar for tulika.kakati
2.8 years ago by
tulika.kakati10 wrote:

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 • 918 views
ADD COMMENTlink modified 2.8 years ago by Nicolas Rosewick7.6k • written 2.8 years ago by tulika.kakati10

Your post is a question, not a tutorial. Please see How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking for details on post types.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by RamRS21k

Thank you !! I am new to this forum.

ADD REPLYlink written 2.8 years ago by tulika.kakati10
1

Please use ADD REPLY or ADD COMMENT when posting a reaction to a previous post, as such we keep this thread logically structured.

ADD REPLYlink written 2.8 years ago by WouterDeCoster39k

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

ADD REPLYlink written 2.8 years ago by WouterDeCoster39k
1
gravatar for Nicolas Rosewick
2.8 years ago by
Belgium, Brussels
Nicolas Rosewick7.6k wrote:

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

ADD COMMENTlink written 2.8 years ago by Nicolas Rosewick7.6k
1

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

ADD REPLYlink written 2.8 years ago by WouterDeCoster39k

Good point, but it could be a simple species.

HIV-1 itself is only 10 genes: http://www.ncbi.nlm.nih.gov/genome/10319

ADD REPLYlink written 2.8 years ago by igor7.6k
1

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

ADD REPLYlink written 2.8 years ago by WouterDeCoster39k
1

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

ADD REPLYlink written 2.8 years ago by igor7.6k
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