Hello, I am doing an meta analysis project with a group and we are having issues with POE and metaArray. poe.fit function is not found for any of us, so we are using poe.em. library(simpleaffy) library(metaArray) library(Biobase) library(MergeMaid) data1 <- read.affy("treat1.txt") eset1 = call.exprs(data1, "rma") #22283 features, 22 samples cl1 = as.numeric(data1$Cancer == "Y") #Create class label data1centered = t(scale(t(exprs(eset1)))) #Center and scale eset data data1.poe = poe.em(data1centered, cl1, threshold = 1e-05, every= 1000) #perform POE transformation on centered eset data ####repeated for our 3 data sets, resulting in: data1.poe, data2.poe and data3.poe###### The next part is where we are stuck common = intersect(rownames(data1.poe), rownames(data2.poe)) common = intersect(common, rownames(data3.poe)) summary(common) Length Class Mode 0 NULL NULL common NULL data1.poe = data1.poe[match(common, rownames(data1.poe)), ] ####Can't use since 'common' is empty Error in data1.poe[match(common, rownames(data1.poe)), ] : incorrect number of dimensions We are using the code from the metaArray vignette to guide us but are stuck on this part. Any help would be appreciated. Sheena > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133acdf_2.6.0 MergeMaid_2.20.0 MASS_7.3-6 survival_2.35-8 [5] metaArray_1.24.0 simpleaffy_2.24.0 gcrma_2.20.0 genefilter_1.30.0 [9] affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 [4] Biostrings_2.16.9 DBI_0.2-5 IRanges_1.6.17 [7] preprocessCore_1.10.0 RSQLite_0.9-2 tools_2.11.1 [10] xtable_1.5-6 [[alternative HTML version deleted]]