Question: RNA seq data analyses
0
gravatar for saj98
2.4 years ago by
saj98100
saj98100 wrote:

Hello everyone

I have RNA seq data from two different experiments, but both experiments are related to one factor (alcohol effect). The first one has been done on tissue and the second experiment has been done on cells. I am interested to find a group of genes related to the alcohol effect vs the control groups. Any suggestion or idea about which analyses I should use.

Thanks for help Shaima

rna-seq R • 566 views
ADD COMMENTlink written 2.4 years ago by saj98100

I used cummeRbund to look for genes expression and sig genes. I am interested to do cross-species analyses to get the significant genes are related to alcohol effect.

ADD REPLYlink written 2.4 years ago by saj98100
3
gravatar for VHahaut
2.4 years ago by
VHahaut1.1k
Belgium
VHahaut1.1k wrote:

Have thought about using a differential expression analysis?

Using a program such as DESeq2/edgeR/Limma to compare your tissues with or without treatment ( ~ alcohol_treatment) and your cells with or without treatment ( ~ alcohol_treatment) separately. Then looking in those two analysis which genes are statistically significant in your two experiments and take them as best candidates?

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by VHahaut1.1k
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