Question: Most diff exp genes are up-regulated... can this be true?
6.8 years ago by
Peter Davidsen • 210
Peter Davidsen • 210 wrote:
Dear List, I'm analysing some one-color microarray data generated using a custom designed Agilent array (their 8 x 60K platform). When I compare control samples to treated ones most (i.e. >80%) of the differentially expressed transcripts are up-regulated. This pronounced up-regulation is independent of type of treatment. I have never before experienced such a quantitative difference in the number of up- and down-regulated transcripts. Furthermore, I have tried to analyse relevant datasets in the GEO that mimics my study design in terms of treatment regime, duration of treatment ect. These analyses--all in closely related species--suggest that the fraction of up and down-regulated transcripts should be roughly the same. The QC reports generated by the Agilent Feature Extraction Software indicate that the data quality should be fine. Also a few basic boxplot before and after normalization haven't raised my suspicion. I do, however, find that the median signal intensity for each sample is significantly lower than what I've seen in the past with the same platform (although targeted against another related species). I have tried to normalize my data using both quantile and vsn, respectively, with similar result. I have also tried to filter my dataset using different intensity filters - again with similar result. And finally, I also tried using both limma and SAMR for the statistics. Have anyone by any chance experienced something similar, and how did you deal with this issue of many siggenes going in one direction? Many thanks, Peter
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