I have mRNA microarray data analysis from both Affymetrix (Hu Gene 2.1 microarray) and Agilent (Human Gene Expression 4×44 K Microarray Kit (Design ID 014850, Agilent Technologies). Is it possible to compare them using Genespring? I have .chp files for Affymetrix and .txt files for Agilent microarray. I want to use them simulteonusly. Briefly, I will compare data obtained from Affymetrix (Hu_Gene 2.1 microarray) vs another data obtained from Agilent (Human Gene Expression 4×44 K Microarray Kit (Design ID 014850, Agilent Technologies) using Genespring, if possible.
Hi Emre
I meet the same problem with 2 different designs in geenspring. the problem is that this soft do not allow the analysis of different designs in the same analysis. On the other hand, affy and agilent do not follow the same bias and the probes are not the same, the risk is that analyzing both technologies give you false results.
fred
Thanks for your answer Fred. I contacted with Genespring and they said that " You could create two different experiments for the different platforms i.e., one experiment with HuGene 2.1 technology and the other with the Agilent technology in the same project.
Once the experiments have been created, you can perform the analysis individually on the two experiments and use the Venn diagram option available in the toolbar to compare the results (entity lists)."
yes of course but don't forget that detected differenced genes will be by different ways (probes are not the same and their affinity/efficiency/...are not the same) and bias. just be careful on the results, they should not describe the differences between both technologies.
all the best
fred
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