Dear Members of the list,


(I apologize for posting this again -I sent it earlier to the list but from another account and I was listed me as non-Member -and Member I am since 2008:-)).


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

modeling 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)

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