Question: Principle Component Analysis input
gravatar for srfr
9 weeks ago by
srfr10 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
ADD COMMENTlink modified 9 weeks ago by mtekman8910 • written 9 weeks ago by srfr10
gravatar for mtekman89
9 weeks ago by
mtekman8910 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 COMMENTlink written 9 weeks ago by mtekman8910

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 REPLYlink written 8 weeks ago by srfr10
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