Hi
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 ?
Thanks
Regards
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 ?
Thanks
Regards
Yes