[BioC] Limma question_Intra-Spot Correlation Question

[jgomez at uni-potsdam.de]

Dear List,
I have a set of Agilent chips that I would like to analyse following  
the procedure for separate channel analysis.
I just want to add that following the brief procedure outline in Limma  
User Guide wasn't useful.
I have made the targets file as usual
  FileName   Cy3   Cy5
1 US83800208_252412610022_1_4.txt  WT_4  OX_4
2 US83800208_252412610019_1_1.txt  KD_4  WT_4
3 US83800208_252412610019_1_2.txt  OX_4  KD_4
4 US83800208_252412610019_1_3.txt OX_21  OX_4
5 US83800208_252412610019_1_4.txt WT_21  WT_4
6 US83800208_252412610020_1_1.txt  KD_4 KD_21
7 US83800208_252412610020_1_2.txt WT_21 OX_21
8 US83800208_252412610021_2_1.txt KD_21 WT_21
9 US83800208_252412610020_1_3.txt OX_21 KD_21
I read the chips using read.maimages and creating an RG object along  
the way. Then I normalized the arrays using Aquantile (Normalization  
Between Arrays). I convert the targets file and then looks like this:
  channel.col                        FileName Target
1.1           1 US83800208_252412610022_1_4.txt   WT_4
1.2           2 US83800208_252412610022_1_4.txt   OX_4
2.1           1 US83800208_252412610019_1_1.txt   KD_4
2.2           2 US83800208_252412610019_1_1.txt   WT_4
3.1           1 US83800208_252412610019_1_2.txt   OX_4
3.2           2 US83800208_252412610019_1_2.txt   KD_4
4.1           1 US83800208_252412610019_1_3.txt  OX_21
4.2           2 US83800208_252412610019_1_3.txt   OX_4
5.1           1 US83800208_252412610019_1_4.txt  WT_21
5.2           2 US83800208_252412610019_1_4.txt   WT_4
6.1           1 US83800208_252412610020_1_1.txt   KD_4
6.2           2 US83800208_252412610020_1_1.txt  KD_21
7.1           1 US83800208_252412610020_1_2.txt  WT_21
7.2           2 US83800208_252412610020_1_2.txt  OX_21
8.1           1 US83800208_252412610021_2_1.txt  KD_21
8.2           2 US83800208_252412610021_2_1.txt  WT_21
9.1           1 US83800208_252412610020_1_3.txt  OX_21
9.2           2 US83800208_252412610020_1_3.txt  KD_21
When using the function intraspotCorrelation I got an error regarding
" Missing or infinite values found in M or A".
Checking older post regarding the erro, it may be becaouse few probes  
have after normalization negative intensities.
I would like to know if the process I started is the right one for  
this kind of analysis and second If there is a kind of filter I can  
use in limma to get rid of those neg intensities to proceed to the  
next step.
Thanks in advance for any help.
Cheers,
Judy

-- 
Judith Lucia Gomez, PhD
Centre for Plant Biotechnology and Genomics - CBGP
28223 Pozuelo de Alarcón (Madrid)
Spain