The limitation with the combine() function is that you are leaving the clinical annotations behind.

InSilico DB has a "merging" R-Bioconductor package to combine public datasets from GEO and their clinical annotations. If you are not using R you can also combine data from the online platform (See this short step-by-step tutorial)

Example:

# Retrieve 2 datasets
eset1 = getDataset(gse="GSE10072", gpl="GPL96", norm="ORIGINAL", genes=TRUE);
eset2 = getDataset(gse="GSE7670", gpl="GPL96", norm="ORIGINAL", genes=TRUE);

#combine them
esets = list(eset1, eset2);
eset = merge(esets, method="NONE");

#plot them
plotMDS(eset, targetAnnot="Disease", batchAnnot="Study");

InSilico DB packaged various batch removal effects methods so line 4 could be replaced with:

eset = merge(esets, method="XPN");

or

eset = merge(esets, method="COMBAT");

Hope this helps.

For more info Bioinformatics paper reference; InSilico DB and InSIlico Merging packages links, and blog link.

• Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages -BMC Bioinfomatics
• inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO - Bioinformatics
• Tutorial example

R-Bioconductor packages:

• http://www.bioconductor.org/packages/2.12/bioc/html/inSilicoDb.html; and
• http://www.bioconductor.org/packages/2.12/bioc/html/inSilicoMerging.html