This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error in read.celfile.header(x)

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
• 2,066 views • link
updated by cpad0112 cpad0112 • written by xxxxxxxx • xxxxxxxx

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

• 0 views • link
written by cpad0112 cpad0112

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

• 0 views • link
written by xxxxxxxx • xxxxxxxx

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.

• 0 views • link
written by Kevin Blighe Kevin Blighe

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

• 0 views • link
written by cpad0112 cpad0112

0 answers

No answers yet.

Log in to answer this question.

More posts like this