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Question: 3-D PCA plot
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gravatar for shuo.li
2.2 years ago by
shuo.li • 10
Australia
shuo.li • 10 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 • 562 views
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modified 2.2 years ago by y.hoogstrate • 460 • written 2.2 years ago by shuo.li • 10
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.2 years ago by shuo.li • 10
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gravatar for y.hoogstrate
2.2 years ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 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 COMMENT • link modified 2.2 years ago • written 2.2 years ago by y.hoogstrate • 460
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