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]]

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]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu