Two channel (Cy3, Cy5) microarray data analysis from Agilent after treatment with Ixazomib and Ursolic Acid on immortal human cell line

Power of each microarray experiments with 8 biological replicates and 50571 transcripts

## $power
## [1] 0.7672424

Reading two-color intensity data with selected annotation information:

## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_1_1.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_1_2.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_1_3.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_1_4.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_2_1.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_2_2.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_2_3.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/Ix_2_4.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_1_1.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_1_2.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_1_3.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_1_4.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_2_1.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_2_2.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_2_3.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/UA_2_4.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_1_1.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_1_2.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_1_3.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_1_4.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_2_1.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_2_2.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_2_3.txt 
## Read /home/kubuntu/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/data/IxUA_2_4.txt

Reading the Spot Type File (STF):

## Matching patterns for: SystematicName ControlType 
## Found 62976 cDNA 
## Found 58717 cDNA 
## Found 2730 ERCC_DQ 
## Found 210 ERCC_EF 
## Found 420 ERCC 
## Found 308 3xSLv1 
## Found 156 ETG 
## Found 36 DCP 
## Found 14 GE_BrightCorner 
## Found 35 DarkCorner 
## Found 35 Control_1 
## Found 35 Control_n11 
## Found 35 Control_a20 
## Found 35 Control_3 
## Found 35 Control_a104 
## Found 35 Control_a107 
## Found 35 Control_a135 
## Found 35 Control_a22 
## Found 35 Control_a97 
## Found 35 Control_n9 
## Setting attributes: values ID Color SubTypeMask

Raw data

Within array loess normalization

## Array 1 corrected
## Array 2 corrected
## Array 3 corrected
## Array 4 corrected
## Array 5 corrected
## Array 6 corrected
## Array 7 corrected
## Array 8 corrected
## Array 9 corrected
## Array 10 corrected
## Array 11 corrected
## Array 12 corrected
## Array 13 corrected
## Array 14 corrected
## Array 15 corrected
## Array 16 corrected
## Array 17 corrected
## Array 18 corrected
## Array 19 corrected
## Array 20 corrected
## Array 21 corrected
## Array 22 corrected
## Array 23 corrected
## Array 24 corrected
## Array 1 corrected
## Array 2 corrected
## Array 3 corrected
## Array 4 corrected
## Array 5 corrected
## Array 6 corrected
## Array 7 corrected
## Array 8 corrected
## Array 9 corrected
## Array 10 corrected
## Array 11 corrected
## Array 12 corrected
## Array 13 corrected
## Array 14 corrected
## Array 15 corrected
## Array 16 corrected
## Array 17 corrected
## Array 18 corrected
## Array 19 corrected
## Array 20 corrected
## Array 21 corrected
## Array 22 corrected
## Array 23 corrected
## Array 24 corrected

Between array aquantile normalization by each experimental group

Outliers not found using MAD (median absolute deviation from the median):

The batch effect between experimental groups:

## Found unique target names:
##  Ix IxUA Ref UA

Analysis with weights:

## 'data.frame':    48 obs. of  6 variables:
##  $ channel.col: num  1 2 1 2 1 2 1 2 1 2 ...
##  $ SlideNumber: int  1 1 2 2 3 3 4 4 5 5 ...
##  $ Name       : chr  "Ix1.1" "Ix1.1" "Ix1.2" "Ix1.2" ...
##  $ FileName   : chr  "Ix_1_1.txt" "Ix_1_1.txt" "Ix_1_2.txt" "Ix_1_2.txt" ...
##  $ Date       : chr  "17/10/2014" "17/10/2014" "17/10/2014" "17/10/2014" ...
##  $ Target     : Factor w/ 4 levels "Ix","IxUA","Ref",..: 1 3 1 3 1 3 1 3 1 3 ...

Considering use {DALEX} as XAI for selecting the best model from: fitnb, fit, fit2, and fitcw.

For further consideration, we used fit2 (separate channels Cy3 and Cy5) model solely:

This step is essential for proper performing Gene Set Enrichment:

fitt2<-fit2
EGID <- read.csv("~/RfromKubuntu/R/Projects/Ix&UA&IxUA--ClearCode/EGID.txt", row.names=1, sep="", stringsAsFactors=FALSE)
EGID <- as.character(EGID[,1])
rownames(fitt2@.Data[[1]])<-EGID

Gene Ontology and KEGG Enrichment Analysis:

Increased genes expression of mostly affected pathways by Ix:

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Up regulated expression

Decreased genes expression of mostly affected pathways by Ix:

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Down regulated expression

Decrease expression of differentialy expressed genes with adjusted p-value 0.05 and fold change 1.5:

Chromosome 21

Interactive heatmap

Chromosome 18

Interactive heatmap

Chromosome 13

Interactive heatmap

Chromosome 1

Interactive heatmap

Now I am working with {UMAP} and {CRPClustering} for clustering differentialy expressed transcripts by chromosome loci