MA plot interpretation before and after normalization
I have a RNA-seq dataset of tumor and control samples. I plotted two MA plots, before and after normalization (plotSmear with Bioconductor). I don't understand how to know it the results are ok just by looking at the shape. My professor explained that if the 'dot cloud' has a trumpet shape, it is good. But then in some exercise examples he shows MA plots with different shapes that are also ok. I would appreciate an explanation for 'dummies' on this as I am a newbie. I forgot to say that I have already read the wikipedia page about MA plots and some articles about RNA-seq with no luck. Thanks in advance.
• 4,367 views
•
link
updated
by
BioinfGuru
•
written
by
Expe •
•
written
by
Expe •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
My PCA plot is weird: PC1 with 98.684% variance and PC2 with 0.582% variance
written by undergrad_student •
-
Seeking Help with Unexpected MA Plot Output
written by Pumla •
-
How PCR amplification affects rna-seq data
written by Javad
-
When to use plotMD() vs maPlot() vs plotSmear()?
written by MLee •
-
ERCC spike-in analysis
written by anilkumar.vijjamarri •
-
RNA-seq Experiment - Multiple Gene names with "." - How can i deal with these
written by drsami
-
Seurat FeaturePlot: highlight only cells coexpressing several genes
written by yassin •
-
STAR - working with binary files in MacOS
written by saraG •
-
Deseq plots interpretation
written by phur •
-
Cuffdiff Strange Output
written by jenny.ditommaso •
It would be better to give an image of the plots in question.
If you can't provide that then please tell us what are your X and Y axis labels?
Sorry for my late reply. The X label is logCPM and the Y label logFC (tumor-control).