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

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