[BioC] Simpleaffy problem

weinong han hanweinong at yahoo.com
Fri Sep 23 06:10:29 CEST 2005

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

Seth Falcon <sfalcon at fhcrc.org> wrote:
On 22 Sep 2005, hanweinong at yahoo.com wrote:
> Hi, everybody
> Procedure as below:

Please tell us the output of sessionInfo() so we can have some
information about your platform and version info.

> 1. Create a directory "npc", move all the relevant CEL files to the
> directory
> 2. Create a covdesc file(see attachment) and put it in the same directory
>> library(simpleaffy)
>> raw.data <- read.affy()
> Error in file(file, "r") : unable to open connection
> In addition: Warning message:
> cannot open file './covdesc' 

What does getwd() say?
How about dir()?

+ seth

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Best Regards
Han Weinong  


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