I have problem on run the function "runMetaAnalysis" from MetaIntegrator package after subset specific genes or probes.
This is my codes:
geo.objects <-c("GSE51387", "GSE64660")
geo.object <-getGEOData(geo.objects, formattedNames = geo.objects, qNorm = FALSE)
probeIDs_of_interest <- c("A_51_P385099", "A_51_P283759", "A_52_P32733",
"A_52_P569539", "A_52_P582969", "A_51_P482552",
"A_52_P229471", "A_52_P249424", "A_52_P638895",
"A_51_P458168", "A_52_P436628")
geo.object$originalData$GSE51387$keys<-geo.object$originalData$GSE51387$keys[names(geo.object$originalData$GSE51387$keys) %in% probeIDs_of_interest]
geo.object$originalData$GSE51387$expr <-geo.object$originalData$GSE51387$expr[probeIDs_of_interest, ]
geo.object$originalData$GSE64660$keys<-geo.object$originalData$GSE64660$keys[names(geo.object$originalData$GSE64660$keys) %in% probeIDs_of_interest]
geo.object$originalData$GSE64660$expr <-geo.object$originalData$GSE64660$expr[probeIDs_of_interest, ]
metaobject <- runMetaAnalysis(geo.object)
The error appeared is:
metaobject <- runMetaAnalysis(geo.object)
Warning: The probes listed in expr and the probes listed in keys do not match.Warning: The probes listed in expr and the probes listed in keys do not match.Warning: $originalData contains some datasets that either are null, the wrong type, or have mismatched samples. These are the datasets: GSE51387 GSE64660Error in runMetaAnalysis(geo.object) : Error in the input object!