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Question: Principle Component Analysis input
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gravatar for srfr
9 weeks ago by
srfr • 10
srfr • 10 wrote:

I have multiple single-cell RNA-seq samples for which I have a generated a featureCount output for each sample. Now I want to do PCA, but it requires a single dataset input. Please, how do I combine all my featureCount output files into a format that the PCA will accept?
rna-seq • 126 views
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modified 9 weeks ago by mtekman89 • 10 • written 9 weeks ago by srfr • 10
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gravatar for mtekman89
9 weeks ago by
mtekman89 • 10
mtekman89 • 10 wrote:

Hi there,

Most PCA tools would require a matrix as input and not a collection of single-column tables. This is actually easy in Galaxy if you use the Column Join tool, assuming your featureCount tables are all in the same format (which they should be).

After that you should have a matrix (tabular) that you can feed into your PCA
ADD COMMENT • link written 9 weeks ago by mtekman89 • 10
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This didn't work for me at all. It wouldn't allow me to select the appropriate columns. Eventually I found that Multi-Join tool did the job quite well.

ADD REPLY • link written 8 weeks ago by srfr • 10
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