Affymetrix Facility Documentation
Affy Facility Docs Home
Running Chips
Sample Submission
Download Data
Annotate Samples
Get Affy Intensity
Analize Data
Analysis Pipeline
Affy Help Pages
Affy Core Help
SBEAMS Help Pages
Analysis Help Pages
Tutorials and Presentations
Other Resources
Affymetrix Home Page

Download Affy Data

Many Affy files can be downloaded or viewed directly from SBEAMS

To download or view Affy files from a particular project go to the ProjectHome page.

1)Select the project from the drop down located at the top of the page.
2)Click the tab "Data Download" near the top of the page
3)To download files: Select the arrays to retrieve information from. The default is to download all the CEL files from a project
4)The check boxes located under the Affy Tab will select or de-select all the files with that particular extension
5)Once all the files are selected click the button "Get_affy_array_files"
6)Select a location to save the zip file containing all the information selected for downloading
Open Link
Here is a brief description of all the file types available for viewing or downloading from SBEAMS
File ExtensionDescriptionView File DirectlyDownload
CHP CHP. Binary Affymetrix file. CHP files contain probe set analysis results generated from Affymetrix software. NO Yes
CEL CEL. Binary Affymetrix file. The CEL file stores the results of the intensity calculations on the pixel values of the DAT file NO Yes
XML XML. MAGE XML Affymetrix file. Contains information from Affymetrix GCOS Software collected during sample preparation, hybridization, washing and scanning. Yes Yes
RPT RPT. Text report. Contains information about the CHP file, used for basic quality control Yes Yes
R_CHP R_CHP. Text File. Contains Probe set intensity values, calculated by using R/Bioconductor affy mas5.0 algorithms No Yes
JPEG JPEG. Jpeg image of the Affy Chip generated by R using the image method within the affy library Yes Yes
EGRAM_PF.jpg EGRAM_PF.jpg. Electrophoregram image of the Pre-fragmented cRNA Yes Yes
EGRAM_T.jpg EGRAM_T.jpg. Electrophoregram image of the total RNA Yes Yes
EGRAM_F.jpg EGRAM_F.jpg. Electrophoregram image of the fragmented cRNA Yes Yes