Error in t-testing

Question

Error in t-testing

I am having errors with a normal t-test:

  data <- read.table("/Users/vdas/Documents/RNA-Seq_Smaples_Udine_08032013/GBM_29052013/UD_RP_25072013/filteredFPKM_matrix.txt",sep="",header=TRUE,stringsAsFactors=FALSE)

  PGT <- cbind(data[,2],data[,7],data[,24])
  PDGT <- cbind(data[,6],data[,8])
  pval2 <- NULL
  for(i in 1:length(PGT[,1])){
     pval2 <- c(pval2,t.test(as.numeric(PDGT[i,]),as.numeric(PGT[i,]))$p.value)
     print(i)
  }

Mistake:

Error in t.test.default(as.numeric(PDGT[i, ]), as.numeric(PGT[i, ])) : 
  not enough 'x' observations

I can't figure out what went wrong with the vector. Could you tell me? I haven't been able to figure it out.

0

r bioinformatics hypothesis-test

vchris_ngs 06 Aug At 8:39 am

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3 answers

fkliron · Answer 1 · 2013-08-06T10:08:09+0000

Chances are your data matters NA

. For example: -

x<-rep(NA,4)
t.test(x)

Error in t.test.default(x) : not enough 'x' observations

nKandel · Answer 2 · 2013-08-06T12:13:49+0000

From your comment. It looks like the error comes from a missing value. You can exclude missing values by setting na.rm=TRUE

. Ref: - Missing value . Before posting the R question, take a look at How to make a great example of reproducible R?

maximus · Answer 3 · 2013-08-06T12:33:03+0000

To remove values NA

:

> a <- sample(c(NA, 1:5), 20, replace = TRUE)
> a
 [1] NA  1  2 NA  1  5  4  4  3  3  2  4 NA  4 NA NA  1  2 NA  5
> b <- na.omit(a)
> b
 [1] 1 2 1 5 4 4 3 3 2 4 4 1 2 5

Error in t-testing

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