I have 200 isolate of Fungi and each isolate has 6 repetitions of different concentrations of fungicide. I want to calculate EC50 for all samples

General
1

I am a PhD student and I am working on gene resistance in fungus.
I have 200 isolate of Fungi and each isolate has 6 repetitions of different concentrations of fungicide. I want to calculate EC50 for all samples.
Please help me out how can I calculate EC50 value for each isolate with help of R studio.
Thank you

2

I think in general you want to check out the GRmetrics package:
https://bioconductor.org/packages/release/bioc/vignettes/GRmetrics/inst/doc/GRmetrics-vignette.html

From that package, the GRfit() function is probably what you want. Start by looking at how an input table should look like:

library(GRmetrics)
data(inputCaseA)
head(inputCaseA)

Then construct your table accordingly and afterwards feed it into the GRfit() function and get the output via the GRgetMetrics() function

drc_output = GRfit(inputCaseA, groupingVariables = c('cell_line','agent'))
head(GRgetMetrics(drc_output))

For more specific instructions we might need some more infos and an example table with your data.

3

image
image289×552 6.2 KB
exper conc effect
2 0 66.92166667
2 0.001 66.92166667
2 0.01 69.33666667
2 0.1 69.30833333
2 1 24.66666667
2 10 0
3 0 60.78666667
3 0.001 50.81333333
3 0.01 57.70833333
3 0.1 49.67333333
3 1 0
3 10 0
5 0 67.89166667
5 0.001 59.64166667
5 0.01 74.26333333
5 0.1 73.735
5 1 13.85333333
5 10 0

4

Please familiarize your self with our guidelines here #meta:faq, you are supposed to make this kind of questions providing a propper REPRoducible EXample (reprex) that includes sample data on a copy/paste friendly format, for example, this would be your sample data on such a format.

sample_df <- data.frame(
    exper = c(2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5),
    conc = c(0, 0.001, 0.01, 0.1, 1, 10, 0, 0.001, 0.01, 0.1, 1, 10, 0,
             0.001, 0.01, 0.1, 1, 10),
    effect = c(66.92166667, 66.92166667, 69.33666667, 69.30833333,
               24.66666667, 0, 60.78666667, 50.81333333, 57.70833333,
               49.67333333, 0, 0, 67.89166667, 59.64166667, 74.26333333, 73.735,
               13.85333333, 0)
)