Error in read.celfile.header(x)

0

Entering edit mode

3.0 years ago

xxxxxxxx ▴ 20

script-

  raw_data <- oligo::read.celfiles(filenames = file.path(raw_data_dir, SDRF$Array.Data.File),verbose = FALSE, phenoData = SDRF)

Error-

Error in read.celfile.header(x) : Is C:\Users\Subham\AppData\Local\Temp\RtmpqWwX92/Dc6h.04-FWD_251485018671.gpr.txt really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats

package oligo rstudio microarray r • 1.2k views

ADD COMMENT • link updated 3.0 years ago by cpad0112 21k • written 3.0 years ago by xxxxxxxx ▴ 20

1

Entering edit mode

read.celfiles function reads cel or cel.gz. It may not read Dc6h.04-FWD_251485018671.gpr.txt. Currently your input or one of your inputs is: Dc6h.04-FWD_251485018671.gpr.txt

ADD REPLY • link 3.0 years ago by cpad0112 21k

0

Entering edit mode

But all files are in the same format only this file is showing an error?

ADD REPLY • link 3.0 years ago by xxxxxxxx ▴ 20

1

Entering edit mode

Then exclude that file. GPR is not CEL format. Please re-check your study design to ensure that you are processing Affymetrix arrays, which come in the CEL format in their raw state.

ADD REPLY • link 3.0 years ago by Kevin Blighe 87k

0

Entering edit mode

could you please post output from $ ls raw_data_dir ? gpr is genepix format as I understand.

ADD REPLY • link 3.0 years ago by cpad0112 21k

Login before adding your answer.