Nanostring and Affymetrix Gene Expression Analysis
Kidney Transplant Biopsy Samples
Mariel Barbachan
04 February 2022
1 Sample Information
The table below contains the information on the sample equivalents from nanostring and affymetrix data, seven samples present in the nanostring data set are missing from the microarray study: MON146, MON183, MON264, MON346, MON354, MON370, MON498.
2 Read and normalize nanostring data
## Background correcting
## Normalizing
## Calculating Expression
3 Read and normalize Affymetrix data
4 Study Groups
After normalizing the data sets, the samples were divided into Rejection (n = 22) versus Non-Rejection (n = 23) classes for further analysis.
4.1 Exploratory Data Analysis
4.1.1 Nanostring
4.1.2 Affymetrix
5 Differential expression
5.1 Nanostring
5.2 Affymetrix
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6 Feature Importance with Boruta
6.1 Nanostring
print(getNonRejectedFormula(classification))## nano_exp_class ~ ADAM8 + ALDH3A2 + ARHGDIB + CCR3 + TNFRSF17
## <environment: 0x5586ba93d630>6.2 Affymetrix
print(getNonRejectedFormula(classification))## affy_exp_class ~ BMP7 + CD244 + TCL1A + TEK
## <environment: 0x5586bbca2dc0>