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Bioconductor Affy RMA AnaylsisThe user would like to obtain signal values for all probe sets on all chips.
| Obtain CEL files: | Steps to obtain CEL files for your project
| 1) | Log in to SBEAMS/Microarray
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| 2) | Choose the 'Project Home' button on the left side of the screen
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| 3) | Choose the 'Data Download' tab along the top of the page
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| 4) | Make sure you have the appropriate project selected in the project
chooser drop-down on the top of the page--you should see your Affy
chips listed on the page
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| 5) | Check the box under CEL for each chip you'd like to analyze
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| 6) | Click the 'GET_AFFY_ARRAY_FILES' button underneath the chip listing, and save these somewhere on your computer.
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| 7) | Unzip the downloaded file to get the actual CEL files.
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| Use R/Bioconductor: | Use the following steps to set up and run R/Bioconductor:
| 1) | R can be downloaded from
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| 2) | Bioconductor packages can be installed by running within R:
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| source("http://www.bioconductor.org/getBioC.R")
getBioC()
| | 3) | Create a CEL file table, U:/name_for_analysis.list. The first line is the chip name, second line is always blank and starting with the third line are the CEL file names. Here’s an example:
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| Mouse430_2
20040811_01_H1_Healthy_Blood_B6-I_PAXgene.CEL
20040811_02_H2p_Healthy_Blood_B6-I_RBClysis_PosFraction.CEL
20040811_03_Healthy_Brain.CEL
20040811_04_IB_Infected_Brain.CEL
20040812_01_H3p_Healthy_Blood_B6-I_noRBClysis_PosFraction.CEL
20040812_02_I1_Infected_Blood_B6-I_PAXgene.CEL
20040812_03_I2p_Infected_Blood_B6-I_RBClysis_PosFraction.CEL
20040812_04_I3p_Infected_Blood_B6-I_noRBClysis_PosFraction.CEL
| | 4) | Use the following code to use the affy.rma function:
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| source("Z:/Affymetrix/bioconductor/source/affy_funcs.R")
# need to substitute in name of directory to which CEL files were saved from SBEAMS
affy.rma("U:/name_for_analysis.list","U:/ name_for_analysis.txt",”/path/to/CEL/files”)
| | 5) | Results are in U:/name_for_analysis.list , columns contained are probeset ID, log2 signal per each chip/probeset, and several annotation fields.
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