Data analysis can be done in Array Informatics, which is capable of filtering, normalizing and standardizing the data, before clustering and principal component analysis can be performed and several plots may be drawn.
Follow the Array Informatics manual.
Additionally a combination of Excel, R, and Array Tools can be used to filter and normalize the data prior to the identification of differentially expressed genes with SAM.
The latest version of R and relevant R packages can be obtained from
. Alternatively you may use this version:
R 1.6.2 for Windows.zip
. SAM can be downloaded from
may also be downloaded from our web site.
- Start Excel and click on the Array Tools button.
- Create an new Experiment file for the data of the microarrays of your experiment.
- Open the ScanArray Express CSV files (note that the suffix has to be changed to *.txt first).
- You now have the option of importing individual data files or selecting pairs of data files for high and low laser power scans, in which case the saturated values of the high laser scan will be replaced by non-saturated values form the low laser scan.
- Export the data to R. Copy the GAL file and all three other file types that are required into the same directory. The paths of the files are listed in the R Commands.R file and are used by R.
- *.spot files containing the M (ratios) and A (intensities) values.
- A GAL file for R (this file does not contain a header).
- An R Commands.R, that contains a commands script for R.
- An Arrays.txt file, that lists the microarrays of the experiment.
- Start R and copy the contents of the R Commands file into the R Console. R normalized the data, writes it to Rout barcode.txt files and creates several control plots.
- Close R and return to Array Tools. Select a microarrays and import its corresponding Rout file.
- Export your data to SAM
- Make sure the regional settings of your computer are set to English before starting SAM. Start SAM by clicking the SAM button and Choose Response Type: One class Response, Number of Permutations: 1000.
- With the SAM Plot Controller you may set a delta value according to the number of false significant you are prepared to accept, List Significant Genes and List Delta Table.