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…
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 […]
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. […]
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 […]
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 […]
“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 […]
I am using a gene expression dataset collected for 269 patients in 19 different batches, over time. One way to visually inspect batch effects in gene expression measurements is to […]
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