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Old 05-09-2013, 05:37 AM   #1
Location: haifa israel

Join Date: Jun 2011
Posts: 62
Default Cluster analysis of RNASeq data

I have a data set made with 6 developmental time points during development, on a newly assembled transcriptome. We used BLAST2GO to annotate the trasncriptome. In looking for interesting genes or patterns to follow up on, we wanted to perform clustering. Since this is my first move into clustering, does anyone have recommendations? I have no idea how to choose between hierarchial, kmeans, etc (and if kmeans - which k do I choose?)
Any help (even pointing me in the direction of a good intro paper) would be appreciated!
Also- what kinds of normalization do I need to do to preprocess the different stages? I feel that the FPKMs are a bit higher than average in one stage and a bit lower than average in another and have no idea how to deal with this.
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