zqfang / qpcr Goto Github PK

--Hi,

i have a problem with one of my result using 'pcr' R package, below it's my little input file:

Sample_Name Target Ct
DMSO miR124 29.46
DMSO miR124 29.13
DMSO miR124 29.03
DMSO miR16 24.97
DMSO miR16 24.94
DMSO miR16 25.05
ABX464 miR124 27.1
ABX464 miR124 28.09
ABX464 miR124 26.91
ABX464 miR16 25.09
ABX464 miR16 25.21
ABX464 miR16 25.12

gene control=miR16
condition control=DMSO
Gene of interest: miR124

With 'pcr' package i obtain FC(miR124)=3.98

group gene normalized calibrated relative_expression error lower upper
1 ABX464 miR124 2.226667 -1.993333 3.981559 0.6366579 2.5609434 6.190223
2 DMSO miR124 4.220000 0.000000 1.000000 0.2320919 0.8513995 1.174537

but with your tool i found FC(miR124)=5.11:
python qpcrCalculate.py -d test_interest_data.xls -s Sheet1 -i miR16 -e DMSO -o bioRep

                     CT Rep0  CT Rep1  CT Rep2  Ct Mean (old)     Ct SD    Ct Mean  Delta Ct  DDelta Ct  Fold Changes

Sample Name Target Name
96H_ABX464 miR124 27.10 28.09 26.91 27.366667 0.633588 27.005000 1.865 -2.355 5.115942
miR16 25.09 25.21 25.12 25.140000 0.062450 25.140000 0.000 0.000 1.000000
96H_DMSO miR124 29.46 29.13 29.03 29.206667 0.225019 29.206667 4.220 0.000 1.000000
miR16 24.97 24.94 25.05 24.986667 0.056862 24.986667 0.000 0.000 1.000000

I don't know how to explain this difference, do you have a clue ?

thank you so much.

best,

Laurent --