[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:
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

URL quantitation types:

URL data 

More information about the Bioconductor mailing list