How to cite the GTEx project
Originally posted on Bits of DNA:
The GTEx consortium has just published a collection of papers in a special issue of Nature that together provide an unprecedented view of the…
Author Archives: inesdesantiago
Confusion matrix terminology is taxicab trigonometry
Originally posted on Bits of DNA:
What are confusion matrices? In the 1904 book Mathematical Contributions to the Theory of Evolution, Karl Pearson introduced the notion of contingency tables. Sometime around the 1950s the…
How to Use t-SNE Effectively
t-SNE stands for t-Distributed Stochastic Neighbor Embedding (t-SNE) and is a popular technique for dimensionality reduction. The technique was introduced by van der Maaten and Hinton in 2008. T-SNE is […]
Your Biomarker doesn’t work (and a case for reproducible research)!
We have all hear about those “breakthrough biomarkers” that.. simply.. do not work! There have been numerous reports in the literature that investigate why certain biomarkers don’t work after all. […]
FPKM, TPM, RSEM or RPKM!? QC metrics for RNA-seq quantification
There are many quantification methods proposed to quantify expression abundance of genes, transcripts, exons or splicing junctions. But we all want to use the best one, right? Rafael A. Irizarry […]
Too few (or none) differential expressed genes? A way to fix the null hypothesis in DESeq2
I’ve been using DESeq2 for testing for differential expression between samples. It’s always worked great, but for some datasets it is not working correctly. I have a DESeqResults object called […]
Computational Reproducibility – Workshop in Cambridge, UK
“I did this yesterday and it worked!” “I can’t remember which version of this software I used to make this figure” “I can’t reproduce the analysis in this paper” “Why […]
