[R] reproducing Graphpad IC50 in R with drc package

[David Winsemius]

On Sep 23, 2015, at 9:21 AM, Jon Arsenault wrote:

> I've been banging my head against the wall a bit with this and would be
> ecstatic if someone could help.
> 
> Initial data:
> 
>     Response Dose
> 1  285.17      0.125
> 2  377.65      0.250
> 3  438.99      0.500
> 4  338.46      1.000
> 5  227.87      2.000
> 6  165.96      0.010
> 7  302.92      0.125
> 8  418.50      0.250
> 9  464.69      0.500
> 10 301.36      1.000
> 11 213.12      2.000
> 12 160.34      0.010
> 13 306.18      0.125
> 14 435.37      0.250
> 15 451.34      0.500
> 16 319.50      1.000
> 17 219.83      2.000
> 18 172.52      0.010
> 19 306.56      0.125
> 20 439.01      0.250
> 21 469.74      0.500
> 22 318.05      1.000
> 23 223.09      2.000
> 
> The graphpad template that that this normally would be placed in then
> transforms the taking the log(Dose,base=10) and normalizes the Response.
> I've confirmed that I was able to recreate that here:
> 
>   NormResponse  LogDose
> 1        41.011 -0.90309
> 2        72.909 -0.60206
> 3        94.067 -0.30103
> 4        59.392  0.00000
> 5        21.246  0.30103
> 6        -0.108 -2.00000
> 7        47.133 -0.90309
> 8        87.000 -0.60206
> 9       102.932 -0.30103
> 10       46.595  0.00000
> 11       16.159  0.30103
> 12       -2.047 -2.00000
> 13       48.258 -0.90309
> 14       92.819 -0.60206
> 15       98.327 -0.30103
> 16       52.852  0.00000
> 17       18.473  0.30103
> 18        2.155 -2.00000
> 19       48.389 -0.90309
> 20       94.074 -0.60206
> 21      104.674 -0.30103
> 22       52.352  0.00000
> 23       19.598  0.30103
> 
> 
> 
> 
> Now graphpad used 'log(inhibitor) vs. normalized response -- Variable
> slope' which it states to be a 4parameter sigmodial but it gives me very
> different results.

"It" gives you very different results, but what is "it", what does it "give" and what are you comparing it to? You should start by identifying the package you are using, and then present the code. (We cannot read you mind.)

> graphpad gives and IC50 of 0.1560 and drm's LL.4 gives 0.1149 and it wont
> even take the transformed data,just throws an error.
> 
> 	[[alternative HTML version deleted]]

But we can tell see that you are not reading the Posting Guide.

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> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA