Tag: DE-analysis

Often in DE-analysis count values (FPKM or TPM) are log transformed with pseudocounts such as Log2(x+1) or Log2(x+0.1), which is done to avoid negative values. Alas, I have noticed a discrepancy I can’t get my head around. Suppose we have two expression values: 30 and 60. Using normal values, Log2FC…

relationship between DE-genes and DE-trascripts in deseq2 1 Hello everybody, I ran a DE –RNAseq project by star-stringtie2- deseq2 pipline. The prepDE.py was used for generation of transcript matrix and gene matrix. Deseq2 were performed at both gene and transcript levels. At the gene level, 838 DE-genes were identified with…