Gene expression Box Plot

Question

[shawin]

Hi,

I have the below box plot for gene expression, please could you help me with meaning of it

https://ibb.co/meKS76

Thank you

[shawin]

@Kevin, Thank you, it is raw data no normalization. when I normalized it looks like:![enter image description here][1]

https://ibb.co/cu4AS6

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

Answer 1

[Kevin Blighe]

It says the following:

• The vast majority of your data points in each sample have values close to zero, as indicated by the fact that both the median bars and upper/lower quartile perimeters are scrunched up at the zero mark
• There are many outliers in your samples, as indicated by the points outside the upper-quartile perimeter.

It does not look like you are plotting logged values. This looks like FPKM-normalised counts, or normalised counts on the negative binomial distribution.

Not that you can re-generate this without the outliers by specifying outline=FALSE to the boxplot function.

Kevin

[shawin]

@Kevin, Thank you, it is raw data no normalization. when I normalized it looks like:![enter image description here][1]

https://ibb.co/cu4AS6

[Kevin Blighe]

The conclusion:

Normalisation successful ! :)