Case Study

A pharmaceutical company generated gene expression data using the NanoString nCounter assay for five subjects across two timepoints (i.e. 10 samples total).

Task involve assessing the quality control by heatmap and generating a figure showing boxplots of summary statistics (minimum, 25th percentile, mean, median, 75th percentile, and maximum) for each timepoint by gene with overlay of individual data points for each sample.

Task 1. Assessing quality control by heatmap

Positive and Negative Controls for Quality Control

##                            POS_C POS_A POS_F POS_D POS_B POS_E NEG_C NEG_D
## GSM2055823_01_4353_PD_mRNA  5597 60232    72  1321 17943   269     1     6
## GSM2055824_02_4355_PD_mRNA  6110 68027   108  1435 20662   286     1     4
## GSM2055825_03_3366_PD_mRNA  5506 62583    92  1406 19037   287     4     4
## GSM2055826_04_4078_PD_mRNA  5590 61885    78  1312 18853   266     2    10
## GSM2055827_05_4846_PD_mRNA  6183 68191    88  1497 20344   293     7    10
## GSM2055828_06_3746_PD_mRNA  5223 59144    78  1343 17895   249    11     3
##                            NEG_E NEG_A NEG_H NEG_G NEG_F NEG_B
## GSM2055823_01_4353_PD_mRNA    20    20     9     3    14    10
## GSM2055824_02_4355_PD_mRNA    19    20     8     6    15     5
## GSM2055825_03_3366_PD_mRNA    48    21     6     4    15    13
## GSM2055826_04_4078_PD_mRNA    26    18     9     4    13    10
## GSM2055827_05_4846_PD_mRNA    25    14     8     5    13     7
## GSM2055828_06_3746_PD_mRNA    79    17     6     2    12     6

Heatmap showing positive and negative control genes in columns and samples in rows.

Task 2.

The differences between the baseline and post-treatment timepoints for two genes of interest: MCL1 and CXCL1

The gene count data was normalized and a matrix corresponding to timepoints of the respective genes used to create boxplot.

Case Study annotations

## # A tibble: 10 x 3
##    sampleid                   Subject Timepoint     
##    <chr>                        <dbl> <chr>         
##  1 GSM2055823_01_4353_PD_mRNA       1 Baseline      
##  2 GSM2055824_02_4355_PD_mRNA       1 Post-Treatment
##  3 GSM2055825_03_3366_PD_mRNA       2 Baseline      
##  4 GSM2055826_04_4078_PD_mRNA       2 Post-Treatment
##  5 GSM2055827_05_4846_PD_mRNA       3 Baseline      
##  6 GSM2055828_06_3746_PD_mRNA       3 Post-Treatment
##  7 GSM2055829_07_3760_PD_mRNA       4 Baseline      
##  8 GSM2055830_08_3790_PD_mRNA       4 Post-Treatment
##  9 GSM2055831_09_4436_PD_mRNA       5 Baseline      
## 10 GSM2055832_10_4050_PD_mRNA       5 Post-Treatment

MCL1 Data Table

##                           key value       category
## 1  GSM2055823_01_4353_PD_mRNA 12.11       Baseline
## 2  GSM2055824_02_4355_PD_mRNA 11.28 Post_treatment
## 3  GSM2055825_03_3366_PD_mRNA 12.20       Baseline
## 4  GSM2055826_04_4078_PD_mRNA 11.31 Post_treatment
## 5  GSM2055827_05_4846_PD_mRNA 11.83       Baseline
## 6  GSM2055828_06_3746_PD_mRNA 12.74 Post_treatment
## 7  GSM2055829_07_3760_PD_mRNA 11.93       Baseline
## 8  GSM2055830_08_3790_PD_mRNA 12.12 Post_treatment
## 9  GSM2055831_09_4436_PD_mRNA 12.11       Baseline
## 10 GSM2055832_10_4050_PD_mRNA 10.96 Post_treatment

CXCL1 Data Table

##                           key value       category
## 1  GSM2055823_01_4353_PD_mRNA 7.721       Baseline
## 2  GSM2055824_02_4355_PD_mRNA 6.022 Post_treatment
## 3  GSM2055825_03_3366_PD_mRNA 7.852       Baseline
## 4  GSM2055826_04_4078_PD_mRNA 5.555 Post_treatment
## 5  GSM2055827_05_4846_PD_mRNA 7.150       Baseline
## 6  GSM2055828_06_3746_PD_mRNA 9.255 Post_treatment
## 7  GSM2055829_07_3760_PD_mRNA 8.409       Baseline
## 8  GSM2055830_08_3790_PD_mRNA 5.700 Post_treatment
## 9  GSM2055831_09_4436_PD_mRNA 7.451       Baseline
## 10 GSM2055832_10_4050_PD_mRNA 6.000 Post_treatment

Box plots of MCL1 and CXCL1 respectively

Boxplots of summary statistics (minimum, 25th percentile, mean, median, 75th percentile, and maximum) for each timepoint by gene with overlay of individual data points for each sample.