 | | Analyze data from Array Express | | | Question | | | Can I analyze data from Array Express, www.ebi.ac.uk/arrayexpress/ ? | | Answer | Array express supports storage of data in various formats. Both so called raw data and also processed data. Depending on how the data is stored and the data source you can import data into Qlucore more or less directly.
For some data sets it might be required to do preparation and normalization before importing it into Qlucore Omics Explorer.
The FAQ: How to import data (RNA-seq, Illumina, Affymetrix, 10x, Agilent, Wizard, tab separated, csv, txt, bam) gives an overview to the different import options that you have to choose from.
If the data you would like to import is .cel files then you can follow the steps below to also import descriptive information of the samples. This is an example and changes might be required based on the specific data set.
1. Go to Array Express
2. Download raw.zip. Unpack the file. Download xxx.sdrf.txt
3. Start Qlucore Omics Explorer
4. Select File | Open
5. Select the .cel files that you unpacked in step 2. Follow the steps in the import and normalization process. After the import is ready you have the data imported.
6. If you would like to combine data sets you should repeat step 1 and 2 for the second data set before you progress to step 3. Note that the data sets have to be generated using the same Affymetrix array to use this process.
7. If you would like to add sample annotations from the ”sdrf.txt” file you need to update that file slightly. The most straightforward way is to in Qlucore Omics Explorer select File | Export | Sample annotations. That will give a txt file with the names given to the samples during the import process.
8. Open the txt file from step 7 in a spreadsheet program (for instance Excel)
9. Open the ”sdrf.txt” file in a spreadsheet program.
10. Copy the first column from the file in step 8 and place it as the first column in the file in step 9. Save the file in Step 9. Save it as a tab separated text file. Make sure that the right ”Sample identifier” is connected to the correct sample when doing the copy. If there are mismatches the wrong sample annotation will be connected to the wrong sample.
11. Go to Qlucore Omics Explorer and do File|Import|Sample annotations and select the file from step 10. Now you have all sample annotations imported from the ”sdrf.txt” file.
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