[BioC] read.celfiles error

[James W. MacDonald]

Hi Varun,

On 7/22/2014 3:11 PM, VG wrote:
> Hi everyone,
> I am trying to use Gene ST arrays data from this GSE number GSE48191.
> It has .CEL files.
> I used the following command
>
> library(oligo)
> celFiles <- list.celfiles("/home/user/Desktop/GSE48191_Iwasaki_affy/")

This only works if you are reading celfiles from your working directory. 
 From ?list.celfiles:

Note:

      Quite often users want to use this function to pass filenames to
      other methods. In this situations, it is safer to use the argument
      'full.names=TRUE'.

In other words, list.celfiles() by itself will just list all the 
celfiles in a given directory. If you also want to point to that 
directory, you need to include full.names = TRUE.

Alternatively, you can do

setwd("/home/user/Desktop/GSE48191_Iwasaki_affy/")
affyRaw <- read.celfiles(list.celfiles())

Best,

Jim


>
> celFiles
> [1] "GSM1171898_WT1_MoGene-1_0-st-v1_.CEL"
> "GSM1171899_WT2_MoGene-1_0-st-v1_.CEL"
>   [3] "GSM1171900_WT3_MoGene-1_0-st-v1_.CEL"
> "GSM1171901_WT4_MoGene-1_0-st-v1_.CEL"
>   [5] "GSM1171902_WT5_MoGene-1_0-st-v1_.CEL"
> "GSM1171903_KO1_MoGene-1_0-st-v1_.CEL"
>   [7] "GSM1171904_KO2_MoGene-1_0-st-v1_.CEL"
> "GSM1171905_KO3_MoGene-1_0-st-v1_.CEL"
>   [9] "GSM1171906_KO4_MoGene-1_0-st-v1_.CEL"
> "GSM1171907_KO5_MoGene-1_0-st-v1_.CEL"
>
> affyRaw <- read.celfiles(celFiles)
>
> I get this error
> Error: These do not exist:
>       GSM1171898_WT1_MoGene-1_0-st-v1_.CEL
>       GSM1171899_WT2_MoGene-1_0-st-v1_.CEL
>       GSM1171900_WT3_MoGene-1_0-st-v1_.CEL
>       GSM1171901_WT4_MoGene-1_0-st-v1_.CEL
>       GSM1171902_WT5_MoGene-1_0-st-v1_.CEL
>       GSM1171903_KO1_MoGene-1_0-st-v1_.CEL
>       GSM1171904_KO2_MoGene-1_0-st-v1_.CEL
>       GSM1171905_KO3_MoGene-1_0-st-v1_.CEL
>       GSM1171906_KO4_MoGene-1_0-st-v1_.CEL
>       GSM1171907_KO5_MoGene-1_0-st-v1_.CEL
>
> Also since they used Affymetrix Mouse Gene 1.0 ST Array I should use this
> package
> pd.mogene.1.0.st.v1
>
> Any help how can i remove the error and then how can I add Gene Annotation
> to Normalized Expression Output??
>
> Regards
> Varun
>
> 	[[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