Question: Exploratory data anaylsis to detect batch effects
0
gravatar for serpalma.v
3.6 years ago by
serpalma.v20
Germany
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:

https://drive.google.com/file/d/0B82aQne0d_mYX1BGWHhHblgzNUU/view?usp=sharing

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
1
gravatar for h.mon
3.6 years ago by
h.mon26k
Brazil
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
1
gravatar for trausch
3.5 years ago by
trausch1.3k
Germany
trausch1.3k wrote:

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

https://github.com/genomicsclass/labs

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):

http://genomicsclass.github.io/book/

 

ADD COMMENTlink written 3.5 years ago by trausch1.3k
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