What is a “good” number of DE genes to use in order to try to understand the underlying biological phenomena using a pathway analysis? It is clear that in a whole transcriptome experiment that produces 20-30,000 measurements, selecting a list of [...]
Pathway Analysis Best Practices This article will answer three key questions Investigators face when doing pathway analysis. What is the best way to choose the set of differentially expressed (DE) genes in order to get the best results from the [...]
We often hear the following question: "Is there any way to know if the whole pathway or the whole GO is upregulated or downregulated? The results table shows p-values and DE numbers, but I want to know if that [...]
You are a life scientist undertaking cutting edge research that involves experiments in which you collect omics data: transcriptomics, genomics, proteomics, methylation, RNASeq, ATACSeq, single cell, etc. You are working on an exciting and very important problem. You have great [...]
Methylprednisolone effective in treating critically ill patients Almost exactly one year ago, the US was experiencing the first wave of COVID-19. In March 2020, SARS-CoV2 is defying all modern medical knowledge and technology killing people at a rate of 1,500 [...]
In a previous post, I wrote about the importance of storytelling in science. This is the other side of the story, the darker side of storytelling, where you decide the story in advance rather than letting your data guide it. [...]
It's such a familiar scenario: you sit with the scientist or a collaborator to understand their research question, perform the analysis, and present your results. Then, a week later, you get an email asking for a whole new analysis of [...]
Whether we like it or not, we, as scientists, are judged based on our communication skills. Tenure committees, academic hiring teams, award panels: they all pour over our papers, scoring us on both the number of papers and [...]