[BioC] CodeLink Package: Not a Codelink exported file.

Diego Díez ddiez at iib.uam.es
Tue Apr 11 12:48:19 CEST 2006

Dear Srinivas,

the codelink package currently only supports reading data exported  
from Codelink Software as text, not other type of data (including  
exported text from excel files obtained from Codelink Software). I  
don't know how the data in ArrayExpress is stored and if you can  
export it in the original format (taking a fast look at the links you  
provided my guess is no). Can you send me the first 20 lines of one  
of these files to see if it conforms with the Codelink format? If  
not, i can only suggest reading the data directly using standard R  
function such read.table, read.delim, etc. Once you have read it, and  
you have a matrix of intensity values you can apply directly  
normalization functions available in other packages as affy or limma.  
In fact, this is tha way i used to do it initially.



El 11/04/2006, a las 4:50, Srinivas Iyyer escribió:

> dear group,
>  i have a dataset from ArrayExpress. According to the
> authors they used codelink chip with Alexa
> 647-Streptavidin conjugate.  However, the description
> on ArrayExpress says that the experimenters used Axon
> instrument for GenePix format.
> When I try to load in a test file with
> name, Spot_mean, Bkgd_median, I get an error.
> The 23 quantitation types that can  be selected are:
> B6351SD,B6352SD,Autoflag,BPixels,B635,B635CV,B635Mean,B635Median,B635S 
> D,Circularity,Dia,FPixels,F635Sat,F635CV,F635Mean,F635MeanB635,F635Med 
> ian,F635MedianB635,F635SD,F635TotalIntensity,Flags,Normalize,SNR635
> where ',' is a tab.
> Out of 23 columns I selected F635Mean and B635Median
> (Spot_mean, Bkgd_Median respectively).  I tried
> fls = list.files(pattern='TXT',path='.')
>> fls
> [1] "cdlink_test.TXT"
> data <- readCodelink(files=list.files(pattern="TXT"),
> sample.name=NULL, flag=list(M=NA, I=NA, C=NA),
> dec=NULL, type="Spot",preserve=FALSE, verbose=2)
>> data<-readCodelink(fls,sample.name=NULL,
> flag=list(M=NA, I=NA, C=NA), dec=NULL,
> type="Spot",preserve=FALSE, verbose=2)
> Error in readHeader(files[n], dec = TRUE) :
>         Not a Codelink exported file.
> Could any one please help me, if this data is
> processed or raw data. if raw, then what are the
> errors I am committing.
> thanks in advance
> sri
> URL quantitation types:
> http://www.ebi.ac.uk/arrayexpress/query/ 
> dataselection;jsessionid=41B61BD0C846519E3B6B4349F8DC96A4? 
> expid=826113654
> URL data
> http://www.ebi.ac.uk/arrayexpress/query/ 
> dataselection;jsessionid=41B61BD0C846519E3B6B4349F8DC96A4? 
> expid=826113654#processed_data
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