Question: Counts, abundance in Tximport
gravatar for hong
7 weeks ago by
hong0 wrote:


I'm using Tximport for assembling transcript level expression data into gene-level expression data

The tool itself works very well

But In the output there are four columns

                abundance"     "counts"        "length"        "countsFromAbundance"

"58SrRNA" 0 0 23.3529 "lengthScaledTPM" "5S_rRNA" 14.57284 3.60305869154167 12.0402593264594 "lengthScaledTPM" "7SK" 5.30782 1.99999704253414 18.3494 "lengthScaledTPM"

I couldn't figure out the exact defnitition of abundance and counts.

Does it mean that the value in counts column is estimated from value in abundance column by the method in countsFromAbundance ?

What column should we accept as gene-level TPM ?



tximport • 86 views
ADD COMMENTlink modified 6 weeks ago • written 7 weeks ago by hong0

Thanks for you reply Michael

Then how about the counts?

In the Tximport web manual

It's written

"We could alternatively generate counts from abundances, using the argument countsFromAbundance, scaled to library size, "scaledTPM", or additionally scaled using the average transcript length, averaged over samples and to library size, "lengthScaledTPM". Using either of these approaches, the counts are not correlated with length, and so the length matrix should not be provided as an offset for downstream analysis packages."

so that means if we set the countsFromAbundance argument to lengthScaledTPM, Can we accept value in counts column as

lengthscaledTPM ?



ADD REPLYlink written 6 weeks ago by hong0


ADD REPLYlink written 6 weeks ago by Michael Love23k
Answer: Counts, abundance in Tximport
gravatar for Michael Love
6 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

Abundance is the abundance measure from the software, most often TPM but some software output FPKM. You can check by adding the columns and they should equal 1,000,000.

ADD COMMENTlink written 6 weeks ago by Michael Love23k
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