Kzebrows Week 12

Electronic Lab Notebook

First, I accessed the microarray data from [ArrayExpress] and downloaded the files labeled "E-GEOD-32978.sdrf.txt" and "E-GEOD-32978.raw.1.zip"

First we analyzed the data by opening the sdrf.txt file. From examining this file it was apparent that no dye swaps had occurred. We looked at the Comment [Sample_Title] column compared to the Label and FactorValue[TREATMENT] columns and found that each sample/control combo was repeated three times leading to a total of 72 samples, but each control was labeled with Cy3 dye and each treated sample was labeled with Cy5 dye. This was the extent of samples that occurred, which is improper technique, because the dyes have different affinities. This could potentially skew the results but we moved forward with our analysis.

Next, I unzipped the raw data file, which expanded to 36 files. Each file contains a treatment and a control hybridized. We eliminated extraneous columns, leaving behind only Column E ("ID") and Column AS ("Log Ratio 635/535"). Because each file has columns with these titles, Column E was re-labeled "