Msaeedi23 Week 11
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Steps for GenMapp analysis
1. Experimental design-what is the treatment and what is the control
- Biological vs technical replicants- for vibrio control was the untreated strain, technical replicates = splitting a sample, different from biological replicates. Biological replicates are derived from the original strain. *note how many replicates of each. # of chips(microarrays) (for vibrio it was 9, total number of samples)
- Dye swaps, cy3 green dye and cy5 red. note how many swaps. Swaps done to avoid dye playing an effect in replication.
- Draw a diagram to help of how chips were obtained.
- Dye swaps, cy3 green dye and cy5 red. note how many swaps. Swaps done to avoid dye playing an effect in replication.
2. Sample + data relationship. In raw data there should be one file to each chip. Match file name to sample. raw.zip on arrayexpress has one file for each chip. Sdrf.txt open in excel to show whats in the samples-should tell you all of the samples, their matches, and dye swaps.
