Question: RNa-seq RPKM data normalization for clustering
0
gravatar for edianfranklin
2.9 years ago by
edianfranklin0 wrote:

I have a dataset from RNA-seq of genes expression in RPKM, one gene per row and four condition. I need clustering that data with kmeans and hierarchical.

My question is: I have to normalize the dataset with transformation to log(x+1) or can use it directly?

normalization rna-seq rpkm • 2.0k views
ADD COMMENTlink modified 2.9 years ago by seta1.2k • written 2.9 years ago by edianfranklin0

This page gives some pointers for clustering which I found useful: http://www.statmethods.net/advstats/cluster.html

ADD REPLYlink written 2.9 years ago by WouterDeCoster40k

thank you, what about the RPKM data?

ADD REPLYlink written 2.9 years ago by edianfranklin0

RPKM already is a normalization. Should your clustering weigh heavier on highly expressed genes or should al genes be taken into account to the same extent? That's the question you have to ask for log normalization. Log normalization will squeeze all values closer together, limiting the effect of the strongest expressed genes...

ADD REPLYlink written 2.9 years ago by WouterDeCoster40k
0
gravatar for seta
2.9 years ago by
seta1.2k
Sweden
seta1.2k wrote:

It's recommended to normalize with log2-transform and then mean-center the data for creating heatmap based on RPKM.

ADD COMMENTlink written 2.9 years ago by seta1.2k

How the mean-center? I did not understand. Can you explain, please

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by edianfranklin0

OP doesn't want to make a heatmap...

ADD REPLYlink written 2.9 years ago by WouterDeCoster40k

Sorry, you're right. However, many tools that generate heatmap, also cluster data at the same time.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by seta1.2k
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