I have to use your pipeline for micro-array analysis(Title:An end to end workflow for differential gene expression using Affymetrix microarrays). I have successfully executed the R code but the problem is that the results obtained by this pipeline are not replicas of the results mentioned in the research paper. I have used the same dataset that was used in this research article. Can you suggest that why my results are different?

thanks

I am guessing that you're referring to this F1000Research article:

https://f1000research.com/articles/5-1384/

This article is now available as the Bioconductor workflow maEndtoEnd. Complete code to reproduce the workflow is available here:

https://www.bioconductor.org/packages/devel/workflows/html/maEndToEnd.html