Question: Error in inputting multiple illumina microarray idat files to limma
0
gravatar for maria2019
10 months ago by
maria2019100
maria2019100 wrote:

Hi,

I have illumina microarray idat files and I want to read them to limma. Below is my code:

library(limma)

idatfiles = dir(path="File_path", pattern = ".idat")
bgxfile = dir(path = "File_path", pattern = ".bgx")
data = readIDAT(idatfiles, bgxfile)

However, I get the following error:

**Error in readIDAT(idatfiles, bgxfile) : 
  Unable to find file 7963862004_A_Grn.idat7963862004_B_Grn.idat7963862004_C_Grn.idat7963862004_D_Grn.idat7963862004_E_Grn.idat7963862004_F_Grn.idat7963862004_G_Grn.idat7963862004_H_Grn.idat7963862004_I_Grn.idat7963862004_J_Grn.idat7963862004_K_Grn.idat7963862004_L_Grn.idat
In addition: Warning message:
In if (!file.exists(file)) { :
  the condition has length > 1 and only the first element will be used
Execution halted**

Any comment on how I can fix this?

I also tried this:

idatfiles <- list.files(path="File_path", pattern ="\\.idat")

and it did not work either

microarray limma idat R • 332 views
ADD COMMENTlink modified 10 months ago by Gordon Smyth2.0k • written 10 months ago by maria2019100
1

What are the contents of idatfiles and bgxfile? Also, form where did you obtain the data? I processed a handful of Illumina chips relatively recently.

ADD REPLYlink written 10 months ago by Kevin Blighe66k
3
gravatar for Gordon Smyth
10 months ago by
Gordon Smyth2.0k
Australia
Gordon Smyth2.0k wrote:

First problem. The limma function is called read.idat, not readIDAT.

Second problem. You haven't told read.idat (or readIDAT) which directory the files are in, so naturally the function can't find them.

You need

x <- read.idat(file.path("File_path",idatfiles), file.path("File_path",bgxfile"))
ADD COMMENTlink modified 10 months ago • written 10 months ago by Gordon Smyth2.0k
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