Hi all,

I need to analyze a combined dataset of microarrays from two sources. The
arrays for the first cell type is from source1 and the arrays for the other
cell types are from source2. I would like to use the advanced rank product
method to identify the unregulated genes. My "origin" vector and sample
vector are as following. However, by using the following code, I got an
error message as highlighted. I think that the arrays for cell type 1 must
from two sources. Does it mean that I cannot use the advanced RankProd? Does
anyone know the major difference between the normal and advanced RankProd
methods?

Thank you in advance,
Wendy


mergeD.origin   # origin vector
 [1] 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[54] 2 2 2 2 2 2 2 2

mergeD.cl   # sample vector
 [1] 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[54] 0 0 0 0 0 0 0 0

RP.adv.out <- RPadvance(mergeD,  mergeD.cl, mergeD.origin, num.perm = 100,
logged = FALSE, gene.names = rownames(mergeD), rand = 123)
 The data is from  2 different origins

Rank Product analysis for two-class case

Error in OriginxyCall(data, cl, origin) :
  Error: data from different origins should contain data from both classes

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