I'm posting in this forum the methodology for my microarray analysis of GSE45596- Brain Angiogenic Vessels in Alzheimer's Disease. The hope is that the reader can replicate my steps in an easy to understand manner to improve analysis of microarray datasets. This dataset represents a dye-swap design conducted upon brain vessels derived from Alzheimer's Disease patients and normal control patients. Therefore, the odd number samples below represent the control microarray samples and the even number samples represent the dye-swapped (cy3 (Green)/ cy5(red)) case samples. In my first post, I'm sharing the raw files for the following 20 samples:
Probes values are normalized log10 ratio Cy5/Cy3
Sample
GSM1110303
GSM1110305
GSM1110307
GSM1110309
GSM1110311
GSM1110313
GSM1110315
GSM1110317
GSM1110319
GSM1110321[/b]
The dye swap was done as a duplicate for each array. The even-numbered datasets are "paired arrays" where cDNA was labeled with Cy3 for the AD sample and Cy5 for the Normal. Meaning that the cDNA used in GSM303 was used again in a duplicate array as GSM304.
Cy3 AD and Cy5 Normal
Probes values are normalized log10 ratio Cy3/Cy5
Sample
GSM1110304
GSM1110306
GSM1110308
GSM1110310
GSM1110312
GSM1110314
GSM1110316
GSM1110318
GSM1110320
GSM1110322
Using this design in the file attached titled "Comparison" you can view the raw signal intensity values per each color in each certain sample and my calculation for the log normalized expression ratio. When compared with the attached published GEO supplementary file for the 417 significant DEG genes above or below 2.0 Fold change, the values I calculated were replicated for each sample. In the fold change column in the comparison file, you can see my FC calculation average(cases)/average(controls). My next post will have a table of the gold standard comparison between the Genespring FC calculated for the 2865 sig. genes found by the researchers of the study (using asymptomatic T-test) versus my own calculations for FC done in excel.