|Can I import and normalize data from Agilent arrays?|
|Yes you can. Qlucore Omics Explorer handled both one and two channel arrays. You need to export your data using the Feature Extraction Software. More information on how to import data can be found here How to import data (Affymetrix, Illumina, 10x, Agilent, Wizard, tab separated, csv, txt, RNA-seq, bam).|
You can also download annotations for your data from https://earray.chem.agilent.com/.
You then need to select the array you are using and select Action |Download after you have marked the file 'Allannotations'
When you have the file on your computer go to Qlucore Omics Explorer and do file | import | variable annotations. Select the downloaded file.
- Data pre-processing for expression data
- Feature Extraction settings
- File extensions
- How does Qlucore calculate the length of the gene to do the normalization?
- How is the normalization (mean=0, Var=1) done in Omics Explorer?
- How to import data (Affymetrix, Illumina, 10x, Agilent, Wizard, tab separated, csv, txt, RNA-seq, bam)
- Normalization of RNAseq data in Qlucore Omics Explorer
- Normalization using housekeeping genes
- Normalization Z-score (mean=0, var=1) calculations
- Normalizing PCR data
- Quantile normalization and eliminated factors
- Supported data types
- TPM values for RNASeq
- Two colored arrays
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