Question: Exploratory data anaylsis to detect batch effects
gravatar for serpalma.v
3.2 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 • 2.3k views
ADD COMMENTlink modified 3.1 years ago by trausch1.2k • written 3.2 years ago by serpalma.v20
gravatar for h.mon
3.2 years ago by
h.mon23k 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 3.2 years ago • written 3.2 years ago by h.mon23k
gravatar for trausch
3.1 years ago by
trausch1.2k 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 3.1 years ago by trausch1.2k
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