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

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Tue Apr 11 04:50:48 CEST 2006


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,B635SD,Circularity,Dia,FPixels,F635Sat,F635CV,F635Mean,F635MeanB635,F635Median,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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