[BioC] Error: All the CEL files must be of the same type

[James W. MacDonald]

Hi Jerry,

On Thursday, November 07, 2013 12:18:27 PM, Jerry Cholo wrote:
>
>
> Hi everyone,
>
>
>
> While I am running these command lines:
>
> library(oligo)
>
>
>
> celFiles <- list.celfiles()

What do you get from typing

celFiles

at an R prompt right after this?

>
> celFiles <- list.celfiles("expressionData", full.names=TRUE)

What is 'expressionData'? A subdirectory of your working directory? 
Again, what do you get when you type

celFiles

at an R prompt?

>
> Data <- read.celfiles(celFiles)
>
>
>
> I got this error:
>
>
>
> All the CEL files must be of the same type.
>
> Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE

Note that you will get this error in two situations:
1.) The celFiles vector contains the names of different array types
2.) The celFiles vector is empty.

> celFiles <- list.celfiles("somerandomthing", full.names = TRUE)
> celFiles
character(0)
> read.celfiles(celFiles)
All the CEL files must be of the same type.
Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not 
TRUE

>
>
>
> All CEL files are hg-1.1-st-Array.  May someone let me know how I could
> solve this problem.

The BEST way to solve this problem is to figure out for yourself what 
is happening. I realize this list is nice, and you can get answers 
quickly. However, you should think of the help you get here as being a 
limited resource. If it appears you are using more than your fair 
share, then you will find your questions going unanswered.

Best,

Jim


>
>
>
> Thanks,
> Jerry
>
> 	[[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099