from RPubs – by Prasanth A S In order to explain the different methods of normalization and their problems with large array of data, which are assumed to have: most genes are not differentially expressed across conditions. the distribution of ...
Read More »How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets
The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety ...
Read More »RPKM, FPKM and TPM, clearly explained
from StatQuest It used to be when you did RNA-seq, you reported your results in RPKM (Reads Per Kilobase Million) or FPKM (Fragments Per Kilobase Million). However, TPM (Transcripts Per Kilobase Million) is now becoming quite popular. Since there seems ...
Read More »The Impact of Normalization Methods on RNA-Seq Data Analysis
High-throughput sequencing technologies, such as the Illumina Hi-seq, are powerful new tools for investigating a wide range of biological and medical problems. Massive and complex data sets produced by the sequencers create a need for development of statistical and computational ...
Read More »Removing technical noise from single cell RNA-Seq data
Single-cell RNA-seq is a promising technology with broad applications and discerning biological noise from technical noise is critical for correctly interpreting the data (Jaitin, et al., 2014). Recently, statistical methods are developed to model the technical noise from spike-in ERCC ...
Read More »An iteration normalization and test method for differential expression analysis of RNA-seq data
Next generation sequencing technologies are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key to analyzing massive and complex sequencing data. In order to derive gene expression measures and compare ...
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