Question: Normalization in Isoform Expression Visualization
1
gravatar for cilgaiscan
21 months ago by
cilgaiscan50
Turkey
cilgaiscan50 wrote:

I have 30 different gene expression data for 30 different cancers. My gene of interest has 3 different isoforms. I like to visualize their expression levels in a single graph. In order to reduce basal expression of isoforms, which normalization method should I use? Could you help?

rna-seq • 500 views
ADD COMMENTlink modified 21 months ago by Kevin Blighe52k • written 21 months ago by cilgaiscan50

How are you accounting for differences across cancer? - In which format is the data, currently?

Once normalised, per cancer, average the gene's expression over the isoforms, and then plot as a simple, ordered barchart (or something else). On the other hand, you indicate that you have a 30 x 3 data-matrix, in which case I would plot these as a levelplot so that you can easily visually see differences across both isoform and cancer.

Kevin

ADD REPLYlink modified 21 months ago • written 21 months ago by Kevin Blighe52k
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