How To Merge To Raw Microarray Data ?

Question

[avi4you]

hello every one i am a student of genetics doing my masters i am working on Diffrential gene expression in avian influenza virus infection in chicken, we have used microarray to know this. what i want to do is i want to analyze two different microarray raw data with available from public database to compare with my data, but as i am a beginer i dont know how to deal with Raw data normalization to compare them and also dont know how to deal with batch effect . can any one help me regarding this topic.. thank you

[ancient_learner]

I would suggest you to analyse the raw datasets individually without mixing them up. once you get expression profile (for each dataset) then compare it in which ever way you want. If you want info on how to analyse agilent array data you can look for R packages or other available tools.

Answer 1

[Sean Davis]

There is no general approach to deal with your situation. The approaches that might be applicable will depend on the microarray platform, the experimental design, and the questions you want to answer. I would suggest consulting a local bioinformatics collaborator to help you with your questions--it will be much more effective than doing this electronically.

That being said, the Bioconductor project has tools for normalization and preprocessing as well as batch effect removal (if that is even applicable), meta-analysis, and differential expression.

[avi4you]

thank you i will try your suggestion i have two raw microarray data from array express both related to diffrential gene expression in chicken to avian influenza infection using Agilent microarray platform since i have already raw data from array express i want to know how to proceed. thanks