MahShaaban/pcr

Negative lower value while analysing the using standard curve

Navrique opened this issue · 1 comments

Dear @MahShaaban,
thank you a lot for developping this pcr package.
While using pcr analysis with the relative_curve method I got a strange output. The lower column of the output show me a negative value for one sample. I found it strange since the result should be express as expression relative to the control sample, in my case SC5314.
I was thinking it could be very useful to have access to all normalised and calibrated values, especially if you want to show result as box plot and dots. The second advantage would be to check incoherent results. Find below the matter to reproduce my error.
slopes = c(-3.065913, -2.868899)
intercept=c(17.31675, 18.71079)
Reference_groupe="SC5314"
Reference_gene="Cт.Mean.EFB1"
group_var=c(CEC3619, CEC3619, CEC3619, CEC5114, CEC5114, SC5314)
InputValue=
Cт.Mean.EFB1 Cт.Mean.orf19_2713
5 19.9565 22.1486
6 19.9993 22.5788
7 19.6004 22.2507
8 20.0437 36.9872
9 19.4609 36.1748
11 20.2800 21.7199

here is the output tbl from pcr_analysis:
group gene normalized calibrated error lower upper
1 SC5314 Cт.Mean.orf19_2713 8.272646e-01 1.000000e+00 NA NA NA
2 CEC3619 Cт.Mean.orf19_2713 3.692645e-01 4.463681e-01 8.969421e-02 0.2034685 0.6892677
3 CEC5114 Cт.Mean.orf19_2713 3.782855e-06 4.572727e-06 2.041283e-06 -0.5396098 0.5396190

Thanks @Navrique for reaching out.
If possible would you please provide a reproducible example. The example you provide doesn't run. You can use R package reprex for this purpose.