[BioC] Advice with RemoveBatchEffect and Rank Product package

[Osee Sanogo]

Dear Members of the list,

I have been using Rank Prod to analyze Agilent two-color data. However, I
would like to remove the dye effect prior to analysis. I read on the forum
that RemoveBatchEffect should be used in the Limma linear model, a type of
model that is not in Rank Product.

I have two questions:

1) Would it be appropriate to use RemoveBatchEffect to correct for dye
effect prior to running the expression data using Rank Prod?

2) a) If no, what other function could I use to do this?
   b) If yes, I would like a help with the correct design and how to
properly indicate the batch.

Here is my design indicating the two dyes (cy3=-1, cy5=1; T, D, C, BS =are
different areas of the brain):

> design1
   BS  C  D  T
1   0  0  0  1
2   0  0  0 -1
3   0  0  0  1
4   0  0  0 -1
5   0  0  0  1
6   0  0  0 -1
7   0  0 -1  0
8   0  0  1  0
9   0  0 -1  0
10  0  0  1  0
11  0  0 -1  0
12  0  0  1  0
13  0  1  0  0
14  0 -1  0  0
15  0  1  0  0
16  0 -1  0  0
17  0  1  0  0
18  0 -1  0  0
19 -1  0  0  0
20  1  0  0  0
21 -1  0  0  0
22  1  0  0  0
23 -1  0  0  0
24  1  0  0  0
attr(,"assign")
[1] 1 1 1 1

I've tried this (Data_RP are my data, the M values of the expression set):

> DYE_RP<-removeBatchEffect(Data_RP, batch=rep(1,24), batch2=NULL,
design=design1)

but it is returning an error message

" Error in contr.sum(levels(batch)) :
  not enough degrees of freedom to define contrasts"

Please help me correct this code.

Thank you so much for your help.

Osee


-- -- --
Y. Osee Sanogo
Integrative Biology
Institute for Genomic Biology
University of Illinois at Urbana
505 S. Goodwin Ave
Urbana, IL-61801

Tel: 217-333 2308 (Office)
     217-417 9593 (Cell)