Error in read.table function using multiclust
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Entering edit mode
Debashis • 0
@a425541d
Last seen 5 weeks ago
India

Enter the body of text here I am trying to cluster the gene expression data of ADNI(GSE 63060),after making a normalized value file while i am giving input_file function available on multiclust its showing

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input.

please help me if any one knows. Code should be placed in three backticks as shown below

library (Biobase)
library(GEOquery)
library(multiClust)
library(preprocessCore)
library(limma)

######################################
gse <- getGEO(filename="GSE63060_series_matrix.txt.gz")
Case <- gse[,1:39]
AD <- gse[,106:155]
CTL <- gse[,40:106]
AD_Data <- cbind.data.frame(AD,Case,CTL)
normalize = function(x){
  return((x-min(x, na.rm = TRUE))/(max(x,na.rm = TRUE)-min(x,na.rm = TRUE)))
}
norm_data = as.data.frame(apply(AD_Data, 2, normalize))
e <- log2(norm_data)

WriteMatrixToFile(tmpMatrix=e,
                  tmpFileName="GSE63060.normalized.expression.txt",
                  blnRowNames=TRUE, blnColNames=TRUE)
exp_file <- system.file("extdata", "GSE63060.normalized.expression.txt", package= "multiClust")
data.exprs <- input_file(input=exp_file)

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
multiClust • 72 views
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Entering edit mode
@kevin
Last seen 2 hours ago
Naas, Republic of Ireland

Hi,

This data (series matrix file) is quantile-normalised and variance-stabilised, according to the GEO record. So, no log2 transformation required.

You probably just need to do:

library(GEOquery)

gset <- getGEO('GSE63060', GSEMatrix = TRUE, getGPL= FALSE)
if (length(gset) > 1) idx <- grep('GPL6947', attr(gset, 'names')) else idx <- 1
gset <- gset[[idx]]
ex <- exprs(gset)

dev.new(width = 12, height = 6)
hist(ex, breaks = 500)

ss

require(multiClust)
WriteMatrixToFile(tmpMatrix = ex,
  tmpFileName = 'GSE63060.normalized.expression.txt',
  blnRowNames = TRUE,
  blnColNames = TRUE)
data.exprs <- input_file(input = 'GSE63060.normalized.expression.txt')

Kevin

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