Question: Question about MatrixEQTL
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gravatar for mms140130
3.2 years ago by
mms14013060
mms14013060 wrote:

my Question is :

i have the gene expression data =genexpt.txt
column1 is gene name , the rest of the columns are expression values

I followed the steps in the MatrixEQTL website
the following is specifying the data in my working directory

expression_file_name = paste(currwd, "/genexpr.txt",sep="")

then I loaded the expression_file_name as follows:

> gene = SlicedData$new() 
  gene$fileDelimiter = ""      # the TAB
> character gene$fileOmitCharacters = "NA" # denote missing values;
> gene$fileSkipRows = 1          # one row of column labels
> gene$fileSkipColumns = 2       # one column of row labels
> gene$fileSliceSize = 5000      # read file in slices of 2,000 rows
> gene$LoadFile(expression_file_name)

    it gave me the following error
 Error: nzchar(output_file_name) is not TRUE

Can anyone help with that please
snp R gene • 1.2k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by mms14013060

Your delimiter setting seems to be weird. Would you try changing:

gene$fileDelimiter = ""      # the TAB

into

gene$fileDelimiter = "\t"      # the TAB

and try again? If you used another delimiter, please change "\t" accordingly.

Also,

 gene$fileSkipColumns = 2       # one column of row labels

means that you have TWO columns of row labels. Trying changing it to 1 also?

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by shunyip180
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