[BioC] Simpleaffy problem

[James W. MacDonald]

weinong han wrote:
> Hi, Seth Falcon
> 'simpleaffy' V 2.11  R Version 2.1.1 used in the analysis.
> covdesc file edited by the white-space delimited file.
>  
> 
>>library(simpleaffy)          
>>dir()
> 
>  [1] "covdesc"  "G05.CEL"  "G09.CEL"  "G10.CEL"  "G12.CEL"  "G15.CEL" 
>  [7] "G19.CEL"  "GF.CEL"   "GM.CEL"   "H044.CEL" "H05.CEL"  "H07.CEL" 
> [13] "H10.CEL"  "H11.CEL"  "H14.CEL"  "N01.CEL"  "N02.CEL"  "N03.CEL" 
> 
>>getwd()
> 
> [1] "D:/npc"
> 
>>raw.data<- read.affy("covdesc")
> 
> Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
>         line 14 did not have 2 elements
>  
> this time, what wrong with my covdesc files? please see attachment

Just what the error message says - line 14 does not have 2 elements!

>         tissue
> G05.CEL NPC
> G09.CEL NPC
> G10.CEL NPC
> G12.CEL NPC
> G15.CEL NPC
> G19.CEL NPC
> GF.CEL  NPC
> GM.CEL  NPC
> H05.CEL NPC
> H07.CEL NPC
> H10.CEL NPC
> H11.CEL NPC
> H14.CEL NPC
> H044.CELNPC  <- This is line 14. There is no space between the filename and tissue type
> N01.CEL NP
> N02.CEL NP
> N03.CEL NP
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623