Search
Question: Error in virtualArray Please help
0
gravatar for Manvendra.Singh@mdc-berlin.de
4.9 years ago by
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 ***************************************** [[alternative HTML version deleted]]
ADD COMMENTlink written 4.9 years ago by Manvendra.Singh@mdc-berlin.de20
0
gravatar for Manvendra.Singh@mdc-berlin.de
4.9 years ago by
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20131212="" 68741639="" attachment-0001.pl="">
ADD COMMENTlink written 4.9 years ago by Manvendra.Singh@mdc-berlin.de20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 358 users visited in the last hour