data extraction cdna arrays affy arrays. stanford microarray database
Post on 21-Dec-2015
233 views
TRANSCRIPT
![Page 1: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/1.jpg)
Data Extraction
cDNA arrays
Affy arrays
![Page 2: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/2.jpg)
Stanford microarray database
![Page 3: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/3.jpg)
Go into public login select organism and the author
![Page 4: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/4.jpg)
If you chose to display data, you can access raw data
![Page 5: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/5.jpg)
If you chose to display data, you can access raw data
![Page 6: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/6.jpg)
Display data for each slide and download
![Page 7: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/7.jpg)
Or you can chose to data retrieval
![Page 8: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/8.jpg)
Click on data analysis to select experiments to download
![Page 9: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/9.jpg)
Click on data retrieval, use default selections, select gene name, accession etc.
![Page 10: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/10.jpg)
Proceed to data filtering
![Page 11: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/11.jpg)
Retrieve data
![Page 12: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/12.jpg)
Download preclustering file: unnormlalized data
![Page 13: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/13.jpg)
Save unnormalize data as text file
![Page 14: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/14.jpg)
Open data file in excel
![Page 15: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/15.jpg)
Proceed to gene filtering
![Page 16: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/16.jpg)
Click on filter data and download median normalized data
![Page 17: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/17.jpg)
You may chose to download raw data for channel 1 and channel 2 to do other normalizations
![Page 18: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/18.jpg)
Affymetrix Data: Go to GEO
![Page 19: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/19.jpg)
Type in a keyword and select a study
![Page 20: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/20.jpg)
Experimental Series Information
![Page 21: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/21.jpg)
Pubmed
![Page 22: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/22.jpg)
Individual array information
![Page 23: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/23.jpg)
Individual array information
![Page 24: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/24.jpg)
Some have .cel files available as suplementary materials
![Page 25: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/25.jpg)
Other examples of sample files normalized differently: e.g., MAS5
![Page 26: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/26.jpg)
Other examples of sample files normalized differently: e.g., dchip
![Page 27: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/27.jpg)
Other examples of sample files normalized differently: e.g., rma
![Page 28: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/28.jpg)
You can download the normalized or raw (.cel file) data
![Page 29: Data Extraction cDNA arrays Affy arrays. Stanford microarray database](https://reader031.vdocuments.mx/reader031/viewer/2022032201/56649d5e5503460f94a3dad3/html5/thumbnails/29.jpg)
Normalization Methods for raw data
Double channel cDNA (channel intensities)
Affymetrix oligo arrays (.cel files)