Download updated annotation (custom .cdf file)

[hagenaue]

1) Read about microarray and how it works: https://www.news-medical.net/life-sciences/How-Do-Microarrays-Work.aspx http://www.premierbiosoft.com/tech_notes/microarray.html https://link.springer.com/protocol/10.1007%2F978-1-59745-538-1_1

2) Read Manhong Dai & Fan Meng's paper arguing for using updated annotation to determine which transcripts the probes on old microarray chips are targeting: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1283542/

3) Their website with more information: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

4) Finding the appropriate custom .cdf file for this chip for humans on Manhong and Fan's website: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/25.0.0/ensg.asp

5) Adapting the sample code to decipher the microarray data using the custom .cdf...

[hagenaue]

More information:
This section of the code will need to be changed to reflect the microarray chip and new chip definition file name (so not hgu133plus2hsentrezg, something else)

cdf and the chip.

hgu133plus2hsentrezg.db_19.0.2.tar.gz# hgu133plus2hsentrezgcdf_19.0.0.tar.gz# hgu133plus2hsentrezgprobe_19.0.0.tar.gz

install.packages(pkgs = c("hgu133plus2hsentrezg.db", "hgu133plus2hsentrezgcdf", "hgu133plus2hsentrezgprobe"), repos = "http://nmg-r.bioinformatics.nl/bioc")

Changed working directory to where the .cel files are located#setwd("~/Documents/Microarray Gen/Lanz_GSE53987/RawData/GSE53987_RAW")

For DLPFC-only analyses:

setwd("~/Documents/Microarray Gen/Lanz_GSE53987/RawData/JustDLPFC") data2 ReadAffy(cdfname ="hgu133plus2hsentrezg")str(data2)data2

[hagenaue]

Information about where to go on Fan's website (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp)

[hagenaue]

Compare the ExpressionSet created by this analysis (using Fan's custom .cdf) to the one created by Gemma: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=1204