Question: 3-D PCA plot
0
gravatar for shuo.li
16 months ago by
shuo.li10
Australia
shuo.li10 wrote:

Hi,

does anyone know if Galaxy.org can do principle component analysis? my boss asked for a 3-D PCA figure and I have no clue how to do it.

Thanks for any tip on this,

Lucy

plot pca galaxy statistics • 324 views
ADD COMMENTlink modified 16 months ago by y.hoogstrate450 • written 16 months ago by shuo.li10
0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

There are a few tools that do this type of analysis. Search at the top of the tool panel with the keyword "pca" and each will come up. Review the tools forms to find the one that fits your data/goals.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 16 months ago by Jennifer Hillman Jackson23k

Thank you Jen for the reply.

To plot PCA, what type of data do I need?

I uploaded the RNAseq data that I got from service provider, but have not yet trimmed or aligned to human genome. Do I need to do this two things first?

Thanks a lot for your help

Lucy

ADD REPLYlink written 16 months ago by shuo.li10
0
gravatar for y.hoogstrate
16 months ago by
y.hoogstrate450
Netherlands
y.hoogstrate450 wrote:

This answer only applies to RNA-Seq analysis

The DESeq2 wrapper of IUC has a few built-in plots. If I'm not mistaken the MDS or PCA are also included. They only need count-tables from your RNA-Seq experiment as input and the rest is done automatically (estimating log fold changes and using those for MDS, not the read counts). You have to estimate the expression levels in your BAM files first (currently by using htseq-count, featureCounts will be available within a short time too)

ADD COMMENTlink modified 16 months ago • written 16 months ago by y.hoogstrate450
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