Question

please resolve the issue

0

Entering edit mode

sonal • 0

@eb2981a3

Last seen 13 months ago

India

Enter the body of text here

Code should be placed in three backticks as shown below

    enter code here

library (GEOquery)
getGEOSuppFiles("GSE2152")
untar ("./GSE2152/GSE2152_RAW.tar",exdir = "./GSE2152/data")
library(oligo)
library (viridis)
library (limma)
library (hgu)
celfiles <- list.celfiles("./GSE2152/data/",full.names = TRUE,listGzipped = TRUE)
raw.data <- read.celfiles(celfiles)
pData (raw.data)$status<- c(rep("non mutant",15), rep("mutant", 7))
pData(raw.data)
boxplot(raw.data,col ="red", main = " raw probe intensities")
GSE2152.rma <- rma (raw.data)
boxplot(GSE2152.rma,col ="blue", main = " raw probe intensities")
design <- model.matrix(~-1+factor(GSE2152.rma$status))
colnames (design) <- levels(factor(GSE2152.rma$status))
design
fit <- lmFit(GSE2152.rma,design)
contrast.matrix<-makeContrasts(mutant- non mutant)

# include your problematic code here with any corresponding output 

 contrast.matrix<-makeContrasts(mutant- non mutant, levels=design)


# please also include the results of running the following in an R session 
Error: unexpected symbol in "contrast.matrix<-makeContrasts(mutant- non mutant"

sessionInfo( )

gene ExpressionData • 533 views

ADD COMMENT • link updated 13 months ago by James W. MacDonald 65k • written 13 months ago by sonal • 0

2

Entering edit mode

It is more convenient to add a small description of what you are doing and what is the issue here so your post should be improved. Your title is not specific, and it should be enhanced. From what is see, the problem is that you have a variable with spaces non mutant, which is not good practice in bioinformatics. Placing the variable between backticks should solve the issue

ADD REPLY • link 13 months ago Basti ▴ 780

score 1 · Answer 1 · 2023-03-13

You cannot have spaces in the names when using makeContrasts. Even if you do as Basti says, you will get an error because 'non mutant' is not a syntactically valid name. You could do

colnames(design) <- make.names(colnames(design))
contrast.matrix <- makeContrasts(mutant - non.mutant, levels = design)

In addition, please use a reasonable name for your post! It's implied that you would like someone to 'please resolve the issue' when you post. At least make an effort to use a descriptive post name if you want people to help you.