How do you read a MA plot?
An MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.
What do MA plots show?
MA plots are commonly used to represent log fold-change versus mean expression between two treatments (Figure 4). This is visually displayed as a scatter plot with base-2 log fold-change along the y-axis and normalized mean expression along the x-axis.
What is a MD plot?
A mean-difference plot (MD-plot) is a plot of log-intensity ratios (differences) versus log-intensity averages (means). For two color data objects, a within-array MD-plot is produced with the M and A values computed from the two channels for the specified array.
How does DESeq2 normalize?
DESeq2 performs an internal normalization where geometric mean is calculated for each gene across all samples. The counts for a gene in each sample is then divided by this mean. DESeq2 detects automatically count outliers using Cooks’s distance and removes these genes from analysis.
What is RPKM in gene expression?
Reads Per Kilobase of transcript, per Million mapped reads (RPKM) is a normalized unit of transcript expression. It scales by transcript length to compensate for the fact that most RNA-seq protocols will generate more sequencing reads from longer RNA molecules.
What is HT seq?
HTSeq is a Python package that calculates the number of mapped reads to each gene.
What is RNA normalization?
Normalization is an essential step in an RNA-Seq analysis, in which the read count matrix is transformed to allow for meaningful comparisons of counts across samples. Another reason normalization is required is that the proportion of mRNA corresponding to a given gene may change across biological conditions.
How is EdgeR different from de seq?
DESeq and EdgeR are very similar and both assume that no genes are differentially expressed. DESeq uses a “geometric” normalisation strategy, whereas EdgeR is a weighted mean of log ratios-based method. Both normalise data initially via the calculation of size / normalisation factors.
What is the MA plot and what does it show?
The MA-plot is a plot of the distribution of the red/green intensity ratio (‘M’) plotted by the average intensity (‘A’). M and A are defined by the following equations. M is, therefore, the binary logarithm of the intensity ratio (or difference between log intensities) and A is the average log intensity for a dot in the plot.
Why do we need a plot diagram in ELA?
Plot diagrams allow students to pick out major themes in the text, trace changes to major characters over the course of the narrative, and hone their analytic skills. Lessons emphasizing these skills meet many Common Core Standards for English Language Arts ( CCSS.ELA-Literacy ).
How is a MA plot used in genomic data?
(October 2009) An MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.
What is the slope of a MA plot?
To determine whether normalization is needed, one can plot Cy5 (R) intensities against Cy3 (G) intensities and see whether the slope of the line is around 1. An improved method, which is basically a scaled, 45 degree rotation of the R vs. G plot is an MA-plot.