Dear all,

I have been analysing the microarray data for three or more experimental
condition

I have noted a very serious problem in analysis performed in the analysis.
the problem observed is as follows:

I had three experimental condition each with control and experimental
condition, having two replicates each

T1 - control (2 replicates) - experiment (2 replicates)
T2- control (2 replicates) - experiment (2 replicates)
T3-control (2 replicates) - experiment (2 replicates)

When analysis was perfomed for T1, T2 and T3 seperatly such as
Name    FileName    Target
T1_c1    T1c1.CEL    T1c
T1_c2    T1c2.CEL    T1c
T1_s1    T2c3.CEL    T1s
T1_s2    T2c5.CEL    T1s


I have got a list of differetially expressed genes respectively for three
sets.

But when analysis was performed together that from a single Target file

Name    FileName    Target
T1_c1    T1c1.CEL    T1c
T1_c2    T1c2.CEL    T1c
T1_s1    T2c3.CEL    T1s
T1_s2    T2c5.CEL    T1s
T2_c1    T3c6.CEL    T2c
T2_c2    T3c7.CEL    T2c
T2_s1    T4c8.CEL    T2s
T2_s2    T4c9.CEL    T2s
T3_c1    T5c1.CEL    T3c
T3_c2    T5c2.CEL    T3c
T3_s1    T6c1.CEL    T3s
T3_s2    T6c2.CEL    T3s

 and analysed the differetially expressed gene for T1, T2 and T3 I get
totally different results from the results obtained by analysing them
seperatly.

I want to know that whether the expression is averaged over all the chips
therfore giving inconsistent result .between the two methods

I want to know whether this incosistency is problem with bioconductor or I
have understood some of the basic analysis part such as design matrix in
certain wrong way.

I shall be very thankful for anyone who will help me in understanding the
basic concept of analysing microarray data.

-- 
Hemant Ritturaj Kushwaha

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