Entering edit mode
8.8 years ago
Shamim Sarhadi
▴
220
I have 2 gene expression and after merging them with insilicomerging package I want to drow a MDSplot but it needs that my dataset has "study" as a variable, is it possible to add a label such as "study" to my gene expression datasets?
I want to merge two GSE with insilicomerging package in R
library(inSilicoDb)
InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a")
eset1 = getDataset("GSE19804", "GPL570", norm="FRMA", features = "gene", curation = 17470)
eset2 = getDataset("GSE10072", "GPL96", norm="FRMA", features = "gene", curation = 17469)
esets = list(eset1,eset2)
library(inSilicoMerging)
eset_FRMA = merge(esets)
plotMDS(eset_FRMA,colLabel="Disease",symLabel="Study",main="FRMA (No Transformation)")
```
If I use another GSE, when I want to draw MDSplot, my dataset(GSE) should has GSE accession number (=study) as a varaible like above example, for instance if you run varLabels(eset1), you will see that study is one of eset1 variables.
Thanks
