Utilizing R statistical software and Shiny R package I’ve developed web apps for the exploration of RNAseq and epidemiological datasets.

Not all NSAIDs are the same: Differing effects of pain-relieving drugs on cognitive decline in the Alzheimer’s Disease Neuroimaging Initiative dataset.

https://braininflammationgroup-universityofmanchester.shinyapps.io/Rivers-Auty-ADNI/

Citation:
Rivers-Auty J, Mather AE, Peters R, Lawrence CB, Brough D (2018) Use of common pain relieving drugs correlates with altered progression of Alzheimer’s disease and mild cognitive impairment. Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association 14 (7):P1337-P1338

Small, Thin Graphene Oxide is Anti-inflammatory Activating NRF2 via Metabolic Reprogramming. LPS iBMDMs with and without graphene oxide.

https://braininflammationgroup-universityofmanchester.shinyapps.io/GrapheneOxide/

Citation:
Hoyle C, Rivers-Auty J, Lemarchand E, Vranic S, Wang E, Buggio M, Rothwell N, Allan S, Kostarelos K, Brough D (2018) Small, Thin Graphene Oxide Is Anti-Inflammatory Activating Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) Via Metabolic Reprogramming. ACS Nano. DOI: 10.1021/acsnano.8b03642

Haley et al. WT microglia vs NLRP3-/- microglia (not cage mates) https://braininflammationgroup-universityofmanchester.shinyapps.io/NLRP3KOmicroglia/

Dewhurst et al. Liver homogenate and hepatocytes with and without gene deletion https://braininflammationgroup-universityofmanchester.shinyapps.io/Dewhurst-et-al-Correlation/

Tissue-resident macrophages in the intestine are long lived and defined by Tim-4 and CD4 expression
https://braininflammationgroup-universityofmanchester.shinyapps.io/Shaw-et-al-TIM-Macs/

Citation:
Shaw TN, Houston SA, Wemyss K, Bridgeman HM, Barbera TA, Zangerle-Murray T, Strangward P, Ridley AJL, Wang P, Tamoutounour S, Allen JE, Konkel JE, Grainger JR (2018) Tissue-resident macrophages in the intestine are long lived and defined by Tim-4 and CD4 expression. J Exp Med 215 (6):1507-1518. doi:10.1084/jem.20180019

Zinc deficiency and Alzheimer’s disease.

• Hippocampus homogenate – effects of APP/PS1 genotype and zinc deficiency.

• Means+SEM https://braininflammationgroup-universityofmanchester.shinyapps.io/zinc_deficiency_in_alzheimers_disease_whole_hippocampus/
• Correlations https://braininflammationgroup-universityofmanchester.shinyapps.io/Correlation-Zinc-Deficiency-Alzheimers/
• Plaque vs non-plaque tissue – effects of APP/PS1 genotype and zinc deficiency. https://braininflammationgroup-universityofmanchester.shinyapps.io/Plaque-NLRP3-Alzheimer-Zinc/

Citation:
Rivers-Auty J, White C, Beattie J, Brough D, and Lawrence C. 2017. [Poster Presentation] Zinc deficiency accelerates Alzheimer’s phenotype in the APP/PS1 mouse model. Alzheimer’s Research UK Conference. Aberdeen, UK.

A Cohen’s D is a standardized effect size which is defined as the difference between your two groups measured in standard deviations. Because the Cohen’s D unit is standard deviations, it can be used when you have no pilot data. As a general guide a Cohen’s D of 0.3, 0.5 and 0.8 corresponds to mild, moderate and large effect sizes, respectively. However, this depends on the context; for example biomarkers would want the effect size to be at least 2, as biomarkers aren’t useful when the groups overlap.

Example paragraph:

As no pilot data has been collected for these experiments, a standardized effect size was used for the power analysis. For this pilot study we will be aiming to detect a large clinically relevant effect size with a Cohen’s d of 0.8. A power analysis using the two-tailed student’s t-test, Sidak corrected for 3 comparisons, with an alpha of 0.05 and a power of 0.8 was performed. From this analysis it was found that 35 human samples in each group would be required.

Cohen J. 1988. Statistical Power Analysis for the Behavioral Sciences. 2nd ed.Hillsdale: Lawrence Erlbaum Associates.

The calculator is for Sidak corrected multiple t-tests. It’s useful for when you have pilot data and have estimates for the mean of the control group and the standard deviations. It allows you to estimate the number of animals required to detect a range of percentage changes from the control group.

Example paragraph:

A power analysis was performed on the primary measure of probe trial performance in the Morris water maze using an alpha of 0.05, and a power of 0.8. Previously acquired data was used for the analysis which had a mean of 24.59 and a standard deviation of 11.21. The clinically relevant therapeutic effect size of a 60% improvement in the task was chosen. This analysis found an n of 14 mice per group is required for the Sidak corrected post-hoc analysis with 6 comparisons. Accounting for the possibility of 10% attrition an n of 16 was chosen for these experiments.

Cohen J. 1988. Statistical Power Analysis for the Behavioral Sciences. 2nd ed.Hillsdale: Lawrence Erlbaum Associates.