Introduction to

gene expression microarray analysis

Bulk RNA-seq course

Presented by Tran Ba Thien
June 5 2023

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Packages Set-up

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 GEO data

https://doi.org/10.1073/pnas.0905718106 3
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7513
Get GEO data

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ExpressionSet object

assayData: Expression data from microarray experiments (rows:

probes; columns: sample ID)
metadata
• phenoData: A description of the samples in the experiment (rows:
sample ID; columns: description elements)
• featureData: features on the chip or technology used (rows: probes;
columns: features)
• further annotations for the features, for example gene annotations from
biomedical databases (annotation).
experimentData: A flexible structure to describe the experiment.
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phenoData & featureData extraction

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phenoData & featureData extraction

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Download data

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Check and unzip data

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Import data

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Processing

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rma() function?
1. Background subtraction: removing non-specific hybridization or non-specific signal captured by
the microarray probes 🡪 more accurate gene expression measurements

2. Quantile normalization: correcting technical variations and differences in the overall signal
intensity between samples 🡪 similar distribution of intensity values of each sample

3. Summarization: combining the intensities from multiple probes targeting the same gene or
transcript 🡪 reduces the dimensionality, more interpretable representation

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 Quantile normalization

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(142) Quantile Normalization, Clearly Explained!!! - YouTube
 Comparison

Raw

Processed

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Filtering

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 Comparison

Processed

Filtering

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Differential gene expression (DGE) analysis

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Annotation

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Visualization
Heatmap

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Visualization
Volcano plot

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Visualization
Boxplot

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Gene ontology analysis

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Gene ontology analysis

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Thanks for your attention

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