Affymetrix Facility Documentation


		Affy Facility Docs Home

	Running Chips

		Pricing Sample Submission

	SBEAMS

		Download Data Annotate Samples GetExpression Get Affy Intensity

	Analize Data

		Analysis Pipeline MEV

	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

Access the Download Page

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

File Types

Here is a brief description of all the file types available for viewing or downloading from SBEAMS

File Extension	Description	View File Directly	Download
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