i followed this script in R
>library(inSilicoMerging)
>library("inSilicoDb")
>InSilicoLogin("username", "password")
>eset1 = getDataset("GSE5847","GPL96",norm= "ORIGINAL", features = "PROBE", curation = 5159)
>eset2 = getDataset("GSE20685","GPL570", norm="ORIGINAL", features = "PROBE", curation = 18031)
>esets = list(eset1,eset2)
>plotMDS(eset_FRMA,colLabel="Disease",symLabel="Study",main="FRMA (No Transformation)")
and then R show me this error:
Error in `[.data.frame`(pData(eset), , symLabel) :
undefined columns selected
how can i solve this error???
tnx michael
but affter adding
eset_FRMA = merge(esets);
I'm getting the same error again !!!!
You could have a look at the pData of the data sets (see ?plotMDS):
Maybe the names differ and could therefore not be merged correctly...
If the error still persists, contact the authors of the package directly.
hi Michael, i am getting the same error.
Hi 1234anjalianjali1234 that problem was related to clinical data that comes with expression data
check your clinical data, you should know, even if the clinical data and your plot lables(sym or col lable)have difference in one letter it'll give you the same error, also it sensitive to capital or lower case letter in your pData(like my case)
Thanks for the help, it worked. But now I am facing another problem. while validating the data I am getting new error.
it would be great if you can help.