Hi I apply the survival analysis in Survival analysis of TCGA patients integrating gene expression (RNASeq) data
and there the code in below
for (i in 1:dim(new_tum)[1]){
ifsumis.na(new_tum[i,])) < dim(new_tum)[2]){
m <- min(new_tum[i,],na.rm=T)
new_tum_collapsed <- c(new_tum_collapsed,m)
} else {
new_tum_collapsed <- c(new_tum_collapsed,'NA')
}
}
but R gave me the following error
> for (i in 1:dim(new_tum)[1]){
+ ifsumis.na(new_tum[i,])) < dim(new_tum)[2]){
Error: unexpected ')' in:
"for (i in 1:dim(new_tum)[1]){
ifsumis.na(new_tum[i,]))"
> m <- min(new_tum[i,],na.rm=T)
Error: object 'i' not found
> new_tum_collapsed <- c(new_tum_collapsed,m)
Error: object 'm' not found
> } else {
Error: unexpected '}' in " }"
> new_tum_collapsed <- c(new_tum_collapsed,'NA')
> }
Error: unexpected '}' in " }"
> }
Error: unexpected '}' in "}"
can you help why?
I guess the second line should be :
if ( sum ( is.na ( new_tum[i,] ) ) < dim(new_tum)[2]){
To debug your code yourself, don't be afraid to test it pieces by pieces. The error message in this one was kind of explicit too : every open parenthesis should get closed and vice-versa.
Thank you very much, can I ask another question about an error for the same survival analysis
pv <- ifelse ( is.na(s1),next,(round(1 - pchisq(s1$chisq, length(s1$n) - 1),3)))[[1]]
Error in ifelseis.na(s1), next, (round(1 - pchisq(s1$chisq, length(s1$n) - :
no loop for break/next, jumping to top level
can you help correcting this code ,
As the error states, next is to be used within a loop. Type ?next in the R console for more information.
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You have one extra closing
)in second line before<. Remove that and run again.R tells you where the error is... Did you read the message?
You are right. There is a bug in the tutorial code.