Error in `[.data.frame`(pData(eset), , symLabel) : undefined columns selected

Question

[Shamim Sarhadi]

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?

Answer 1

[michael.ante]

It seems you missed

eset_FRMA = merge(esets);

from code chunk #3

[Shamim Sarhadi]

Thanks michael but after adding eset_FRMA = merge(esets);, I'm getting the same error again!

[michael.ante]

You could have a look at the pData of the data sets (see ?plotMDS):

 # check available annotations:
     colnames(pData(eset_FRMA))
     table(pData(eset_FRMA)[,"Disease"]);
     table(pData(eset_FRMA)[,"Study"]);

Maybe the names differ and could therefore not be merged correctly...

If the error still persists, contact the authors of the package directly.

[1234anjalianjali1234]

Hi Michael, I am getting the same error.

[Shamim Sarhadi]

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 labels (sym or col label) 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)

[1234anjalianjali1234]

Thanks for the help, it worked. But now I am facing another problem. while validating the data I am getting new error.

plotGeneWiseDensity(eset_NONE,
  batchAnnot = "Study",
  gene = "MMP2",
  main = "NONE (No Transformation)");

Error: could not find function "plotGeneWiseDensity"

plotDendrogram(eset_NONE,
  batchAnnot = "Study",
  main = "NONE (No Transformation)",
  legend = FALSE);

Error: could not find function "plotDendrogram"

plotGeneWiseBoxPlot(eset_NONE,
  batchLabel = "Study",
  colLabel = "X.Sample_characteristics_ch1",
  gene = gene,
  main = "NONE (No Transformation)");

Error in exprs(eset)[gene, idx] : subscript out of bounds

It would be great if you can help.

Answer 2

[Shamim Sarhadi]

Actually as far as I know insilicomerging package does not support plotGeneWiseDensity and plotDendrogram anymore in the latest version, you could ask insilicodb admin for more information

[Mo]

@Shamim Sarhadi it shows in the error message that getDataset does not exist as a function in the inSilicoMerging package. I suggest you make a small example of your data and then tell what you want to do, so people could help you easier

[1234anjalianjali1234]

@Mo, getDataset is a function in insilicoDB package.