R help - Jun 2011 - Error message

Hi
fn <- dir(pattern="txt",full.name=T)
>  fn
[1]
"./GSM696980_US81503234_252741110209_S01_CGH_107_Sep09_1_1_32914.txt"
[2]
"./GSM696981_US81503234_252741110209_S01_CGH_107_Sep09_1_2_32916.txt"
[3]
"./GSM696982_US81503234_252741110209_S01_CGH_107_Sep09_1_3_33021.txt"
[4]
"./GSM696983_US81503234_252741110209_S01_CGH_107_Sep09_1_4_33024.txt"
> RG <-
read.maimages(fn,source="agilent",quote="",other=c("gProcessedSignal","rProcessedSignal","gProcessedSigError","rProcessedSigError"),
+ columns=list(G = "gMeanSignal",Gb = "gBGMedianSignal", R
="rMeanSignal", Rb = "rBGMedianSignal"))
Error in readGenericHeader(fullname, columns = columns, sep = sep) :
  Specified column headings not found in file


I am trying to read the data into R using read.maimages(), but it is showing me
this error. The data is from agilent and I checked the columns they exist on the
dataset. I am also sending you an array file with this email.
Please comment on this.
Thanking you
Mrutyunjaya Parida



The information transmitted is intended only for the per...{{dropped:10}}

On 06/07/2011 01:38 PM, Parida, Mrutyunjaya wrote:
> Hi
> fn<- dir(pattern="txt",full.name=T)
>>   fn
> [1]
"./GSM696980_US81503234_252741110209_S01_CGH_107_Sep09_1_1_32914.txt"
> [2]
"./GSM696981_US81503234_252741110209_S01_CGH_107_Sep09_1_2_32916.txt"
> [3]
"./GSM696982_US81503234_252741110209_S01_CGH_107_Sep09_1_3_33021.txt"
> [4]
"./GSM696983_US81503234_252741110209_S01_CGH_107_Sep09_1_4_33024.txt"
>> RG<-
read.maimages(fn,source="agilent",quote="",other=c("gProcessedSignal","rProcessedSignal","gProcessedSigError","rProcessedSigError"),
> + columns=list(G = "gMeanSignal",Gb =
"gBGMedianSignal", R ="rMeanSignal", Rb =
"rBGMedianSignal"))
> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>    Specified column headings not found in file
>
>
> I am trying to read the data into R using read.maimages(), but it is
showing me this error. The data is from agilent and I checked the columns they
exist on the dataset. I am also sending you an array file with this email.
> Please comment on this.
This is a Bioconductor package so please ask there.

   http://bioconductor.org/help/mailing-list/

Perhpas not all the files are the same, and the headings are missing 
from some, or the files are produced by different versions of agilent 
software and so have different numbers of headings, or...

Martin
> Thanking you
> Mrutyunjaya Parida
>
>
>
> The information transmitted is intended only for the p...{{dropped:17}}