Please help - object of type 'closure' is not subsettable error!

General
1

Hi all,

I am trying to optimize a PCR reaction but keep getting the error 'object of type 'closure' is not subsettable'.

Does anyone know where this is?
install.packages("readxl")
install.packages("knitr")
install.packages("kableExtra")

library(readxl)
library(knitr)
library(kableExtra)

PCR_REACTION <- read_excel("D:/joey/PCRREACTION.xlsx")
PCR_REACTION$Factors <-c("No.of cycles","Each Dntp",
"Each primer", "Plasmid", "Polymerase")
PCR_REACTION <-PCR_REACTION[,c(4,2,3)]
colnames(PCR_REACTION) <-c("Factor", "+1", "-1")

kable(PCR_REACTION, align = "l", caption =
"Table 1. Factors and Levels Assayed in Fractional Factorial Design") %>%
kable_styling(bootstrap_options = c("striped", "condensed", "responsive",
font_size = 16), position="left") %>%
row_spec(1:5, font_size = 16)
View(PCR_REACTION)

install.packages("AlgDesign")
library(AlgDesign)

Data <- gen.factorial(levels=2,nVars=5,center=TRUE, varNames=c("No.of cycles","Each Dntp","Each primer","Plasmid","Polymerase")

#specify the quarter design using Federov's exchange algorithm and 8 experiments
FFD_quarter <- function(optFederov) {return(~.,data,8) }
FFD_quarter$design <-write.csv(FFD_quarter$design,
file="FFD_quart_design.csv")

2

This code is confusing to me on the grounds that.
the majority of it from the beginning seems oriented around getting and manipulating a PCR_REACTION object
Then you introduce a library(AlgDesign)
The code from this point makes no reference to PCR_REACTION.
So is PCR_REACTION relevant ?

3

I use the alg design library to make the FFD for the analysis

4

I'm not 100% sure, but I think the above line could be causing trouble. It looks like you're missing a closed parenthesis: you have ( after gen.factorial, and then you have another ( after c, but you only have one, not two, )'s after "Polymerase".

Give that a try and see if it fixes things?

5

That fixed another error I was getting but didn't solve the object closure error, thanks so much though!

6

Its not straightforwardly easy to know what causes your error as it's not possible to run your code (it includes data only you have...)
Here is a guide on how you can approach that.

I was asking about the relevance as it seems you have one complaint , but two unrelated codes, I was attempting to identify the problematic code. I hope you understand my intentions.

7

My data is quite simple as im doing a design of experiments approach to find optimal pcr conditions but havent gotten very far without getting an error.
#This is the data im going off

|Factor|Level_Plus|Level_Minus|
|No.of cycles |100 |1|
|tds |5 |8|
|primer | 0. 5 |60|
|membrane| 0.7| 60|
|Polymerase| 0.2 |50|

Thank you! Ill have a read of that page too :slight_smile:

8

@nirgrahamuk

Hi Nir,

I dont suppose you have any more advice to offer regarding this error please? I still havent found a solution (very new to this)

9 
library(AlgDesign)

Data <- gen.factorial(levels=2,
                     nVars=5,
                     center=TRUE,
                     varNames=c("No.of cycles",
                                "Each Dntp",
                                "Each primer",
                                "Plasmid",
                                "Polymerase"))

#FFD_quarter <- function(optFederov) {return(~.,data,8) }
FFD_quarter <- optFederov(~.,Data,8)
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10

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