Entering edit mode
8 months ago
Chris
▴
340
Hi Biostar,
I would like to do differential expression at pathway level by following this tutorial. I have microarray data. Would you please tell me how to get an object like leukimia_eset
? Thank you so much!
data(leukemia)
leukemia_eset
https://bioconductor.org/packages/devel/bioc/vignettes/GSVA/inst/doc/GSVA.html
Thank you so much for the info!
Hi,
I can create an expressionset object but I don't have subtype to run the next step:
My microarray data can classify samples into 2 or 3 sub groups. Do you have any suggestion to add
subtype
into my expressionset object:The
ExpressionSet
object you are building still lacks two key "slots":featureData
andphenoData
. In this context, features refer to information regarding microarray probes. You should have some type of file with probe IDs (depending of the array used) that can be mapped later to genes with packages such as AnnotationDbi.Then, phenotypic data depends on the experimental design of your run. For what you're telling me you can classify your samples in several groups depending on a factor or biological condition you want to study. You should build a
data.frame
whose rows correspond to the columns of the microarray matrix with the samples info (I'm assuming your microarray matrix is in the standard -omics form: rows are different probes and columns are intensities measured for each sample), and add that aspData
. With this, you'd be able to use that factor the same way as the tutorial usessubtype
to build a model matrix for applyinglimma
. This last one is crucial for differential expression analysis in microarrays, so definitely worth to study it carefully before performing any enrichment analysis.There are good
limma
examples in the vignettes of the package, but I'll also leave you some practical example pages:Good luck with your analysis!