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Question: how to perform a Differential gene expression when you don't have any reference matrix?
1
gravatar for Nemo
2.8 years ago by
Nemo60
India
Nemo60 wrote:

Hello,

I have been searching to find a method to define up or down regulated of a set of genes. There are plenty of R packages in Bioconductor. Note that I cannot use any because I only have one matrix. I don't have any reference matrix nor do I have phynotype etc.

Is there any package which allow me to define up or down regulated of my genes ?

 

Thanks  

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Nemo60
1
gravatar for Sean Davis
2.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Up- and down-regulated genes are always defined relatively between two groups of samples.  This is why there are no packages to do such an analysis.  You'll need to come up with one or more questions that you can answer with your data, perhaps starting with some unsupervised analyses (clustering, MDS, etc.).  That said, if you truly know nothing about the samples, then the task of finding important information in your data is that much harder.

ADD COMMENTlink written 2.8 years ago by Sean Davis21k
1
gravatar for Nemo
2.8 years ago by
Nemo60
India
Nemo60 wrote:

@ Sean Davis, what about GSEA? do you think it is possible to perform such analysis ? 

ADD COMMENTlink written 2.8 years ago by Nemo60

No.  GSEA needs a ranked list of genes based on a hypothesis test (or relative fold change).  

ADD REPLYlink written 2.8 years ago by Sean Davis21k
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