Unexpected symbol with code

[Rachel24243]

Hi, I am trying to put this code into R, but it keeps telling me I have an "unexpected symbol."

phenoData<-read.csv("pheno.txt",header=TRUE,sep="\t")design<-model.matrix(~diagnosis,phenoData)fit<-lmFit(eset,design)

Error: unexpected symbol in "phenoData<-read.csv("pheno.txt",header=TRUE,sep="\t")design"

[aguerodev]

Try it this way

phenoData <- read.csv("pheno.txt", header=TRUE, sep="\t")

design <- model.matrix(~diagnosis, phenoData)

fit <- lmFit(eset, design)

[Rachel24243]

Hello,

Yes I tried it this way as well but got the following error.

design <- model.matrix(~diagnosis, phenoData)
Error in eval(predvars, data, env) : object 'diagnosis' not found

[andresrcs]

Hi!

To help us help you, could you please prepare a reproducible example (reprex) illustrating your issue? Please have a look at this guide, to see how to create one:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2…

[Rachel24243]

Thank you for the help!

I realized I specified the data in the txt file as something other than "diagnosis", which is why it was unrecognizable.