Adding a variable as a varlabel to my dataset

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)")

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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

• 352 views • link

updated 3.7 years ago by Ram

• written 11.1 years ago by Shamim Sarhadi

Please explain with a demo of your data. What exactly you want? Do you want a prefix "study" for each gene?

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written 11.1 years ago by Deepak Tanwar

I ran your code above and it worked perfectly, so not sure what problem you are having. Please be more specific and post the code/dataset that you are have problems with so that we can reproduce your problem and suggest a solution.

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updated 3.7 years ago by Ram

• written 11.1 years ago by alolex

Yes those codes work if we change the GSE number it doesn't work e.g if you run this script:

source("http://bioconductor.org/biocLite.R")
library("inSilicoDb")
InSilicoLogin("insilico1365@gmail.com", "1f9d55c6b381079ba4e2374de2d66b3a")
eset = getDatasetInfo("GSE4922", "GPL96")
eset1= getDataset("GSE21422","GPL570",norm= "ORIGINAL", features = "PROBE", curation = 21459)
eset2 = getDataset("GSE4922 ","GPL96",norm= "ORIGINAL", features = "PROBE", curation = 5158)

esets = list(eset1,eset2)
library(inSilicoMerging)

eset_FRMA = merge(esets)

plotMDS(eset_FRMA,colLabel="Disease",symLabel="Study",main="FRMA (No Transformation)")

You will see that "study" is not as a variable in those GSE!

Thanks

• 0 views • link

updated 3.7 years ago by Ram

• written 11.1 years ago by Shamim Sarhadi

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