how to obtain differentially expressed genes from a GSE serie
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Salvo88 ▴ 20
@salvo88-14379
Last seen 2.2 years ago

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

microarray GSE • 444 views
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Salvo88 ▴ 20
@salvo88-14379
Last seen 2.2 years ago

Yes, I did it, now it works perfectly

 

Thank you very much

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@sean-davis-490
Last seen 17 days ago
United States

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.

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