Question: Exploratory data anaylsis to detect batch effects
gravatar for serpalma.v
3.6 years ago by
serpalma.v20 wrote:

Dear members:

I am new at microarray data anaylsis. I am inspecting the log2 transformed data from an affimetrix array and this is the boxplot. 

From what I have read, there seems to be no batch effect since the medians and means are very similar:

How would you interpret this plot and how else can I detect a batch effect?


Thanks for the help!




batch effect microarray • 2.6k views
ADD COMMENTlink modified 3.5 years ago by trausch1.3k • written 3.6 years ago by serpalma.v20
gravatar for h.mon
3.6 years ago by
h.mon26k wrote:

Without labels, it is impossible to say anything meaningful about your data. I don't think boxplots are a good way to explore batch effects, a better way to explore the data are PCA (principal component analysis) or MDS (multidimensional scaling) plots. limma has a function for MDS plots.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by h.mon26k
gravatar for trausch
3.5 years ago by
trausch1.3k wrote:

There is a free HarvardX course on data analysis in the life sciences:

It has lots of exercises in R with real microarray & NGS data and has a full chapter on detecting batch effects and exploratory data analysis (chapter 2 & 10):


ADD COMMENTlink written 3.5 years ago by trausch1.3k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 728 users visited in the last hour