
Dear All,

    I am using virtual array package from R-Bioconductor and can not get the way out of error. I am extremely frustrated since its very important and I require it urgently, Please Please Please help.

  I am doing exactly as it is written to use package,

###### checked that they are in log2 form

GSE46872 <- getGEO("GSE46872")
GSE46872 <- GSE46872[[1]]

GSE21222 <- getGEO("GSE21222")
GSE21222 <- GSE21222[[1]]
> library(virtualArray)
 virtArrays <- list()
 virtArrays[["EB"]] <- virtualArrayExpressionSets()

out put is as follows ,  error is in blue bold
Now preprocessing raw data of GSE21222: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE21222.
Now preprocessing raw data of GSE21222: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE21222: Annotating expression values with SYMBOL...
Size of expression matrix of GSE21222: 19851 rows and 18 columns.
Now preprocessing raw data of GSE46872: Loading annotations...
Usinghugene10sttranscriptclusteras Bioconductor annotation package for datasetGSE46872.
Now preprocessing raw data of GSE46872: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE46872: Annotating expression values with SYMBOL...
Size of expression matrix of GSE46872: 19917 rows and 12 columns.
Now preprocessing raw data of GSE21222: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE21222.
Now preprocessing raw data of GSE21222: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE21222: Annotating expression values with SYMBOL...
Size of expression matrix of GSE21222: 19851 rows and 18 columns.
Now preprocessing raw data of GSE46872: Loading annotations...
Usinghugene10sttranscriptclusteras Bioconductor annotation package for datasetGSE46872.
Now preprocessing raw data of GSE46872: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE46872: Annotating expression values with SYMBOL...
Size of expression matrix of GSE46872: 19917 rows and 12 columns.
Now combining pData of all data sets...
Now setting up pData of GSE21222...
Now setting up pData of GSE46872...
Matching and merging all data sets. This could take some time...
Size of expression matrix of whole dataset: 17545 rows and 30 columns.
Using columns as information for batch effect removal.
Reading Sample Information File
Reading Expression Data File
Found 2 batches
Found 0 covariate(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data
The numbers of overlapping genes/identifiers between each pair of datasets and the final result were as follows:

Error in data.frame(full = c("19851", "19917", "17545"), vs. = c("0",  :
  duplicate row.names:

I would be so obliged and grateful to get a solution

Thanks
Manu


*****************************************
Manvendra Singh
AG Izsvak - Mobile DNA
Room 209, 27: Walter-Friedrich House
Max Delbrück Center for Molecular Medicine
*****************************************

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