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Question: how to obtain differentially expressed genes from a GSE serie
1
gravatar for Salvo88
4 weeks ago by
Salvo8820
Salvo8820 wrote:

Hello everyone,

I have loaded through GEOquery a GSE serie, I used this function from a quick tutorial I found and I just modified with my dataset of interest:

ex:

GSE16444 <- getGEO('GSE16444', GSEMatrix=FALSE)

I tried to transform in a dataset with the  function find in the same tutorial: 

eset <- GDS2eSet(gds,do.log2=TRUE)

my daaset of interest it is a miRNA microarray dataset, what I would like to do is to perform the different express miRNAs between two groups of the dataset. How I should procede? Which packages and function you suggest?

thank you very much for your help

Salvo

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Salvo8820
1
gravatar for Salvo88
4 weeks ago by
Salvo8820
Salvo8820 wrote:

Yes, I did it, now it works perfectly

 

Thank you very much

ADD COMMENTlink written 4 weeks ago by Salvo8820
0
gravatar for Sean Davis
4 weeks ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Use GSEMatrix = TRUE. The result from getGEO is a list, so use only the first element.

GSE16444 <- getGEO('GSE16444', GSEMatrix = TRUE)

The GSE16444 is now an ExpressionSet that can be used in any package that performs differential expression analysis starting from there. Limma is an appropriate choice, but there are many others.

ADD COMMENTlink written 4 weeks ago by Sean Davis21k
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