[BioC] Confusing results

[Jenny Drnevich]

Hi Hemant,

The question was just asked and answered a couple of days ago:

https://stat.ethz.ch/pipermail/bioconductor/2009-February/026349.html

Jenny

At 12:11 PM 2/18/2009, hemant ritturaj wrote:
>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
>
>         [[alternative HTML version deleted]]
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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