Question

Fail to recognize CDF-file

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Jens Vilstrup Johansen ▴ 20

@jens-vilstrup-johansen-114

Last seen 10.2 years ago

This is a multi-part message in MIME format. ------_=_NextPart_001_01C28C84.2D819456 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi I've installed R (version 1.5.1) on my windows machine and used the = install script to install the full Bioconductor package.=20 1. I change the directory to the folder containing my CEL-files and the = CDF-file. 2. I load the 'affy'-package: "library (affy)". OK, so far. 3. I write "Data <-ReadAffy()" and get the following error message:' reading CDF file Error in read.cdffile(CDFfile, compress =3D compress.cdf) :=20 The specified file does not appear to be a CDF file. What has gone wrong? I've attached the CDF-file for U133A that I've used, in case that is the = reason. I'd really appreciate your advice. Thanks! regards, Jens Johansen Nordic Bioscience A/S ------_=_NextPart_001_01C28C84.2D819456 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable <html> <head> <meta http-equiv="3D"Content-Type"" content="3D"text/html;" =="" charset="3Diso-8859-1""> <meta name="3D"Generator"" content="3D"MS" exchange="" server="" version="6.0.5762.3""> <title>Fail to recognize CDF-file</title> </head> <body>

Hi

I've installed R (version 1.5.1) on my = windows machine and used the install script to install the full = Bioconductor package.

1. I change the directory to the folder = containing my CEL-files and the CDF-file.

2. I load the 'affy'-package: = "library (affy)". OK, so far.

3. I write "Data = <-ReadAffy()" and get the following error message:'

reading CDF file
Error in read.cdffile(CDFfile, = compress =3D compress.cdf) : 
 The specified = file does not appear to be a CDF file.

What has gone wrong?
I've attached the CDF-file for U133A = that I've used, in case that is the reason.

I'd really appreciate your = advice.
Thanks!

regards,
 Jens Johansen
Nordic Bioscience A/S

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cdf cdf • 1.0k views

ADD COMMENT • link updated 22.0 years ago by Rafael A. Irizarry ▴ 640 • written 22.0 years ago by Jens Vilstrup Johansen ▴ 20

score 0 · Answer 1 · 2002-11-15

sorry for the late response. regarding your bug report about write.exprs... i wrote it so that it behaves similar to write.table. if you look at the help file for write.table you will see that the following does what you want: creates a file that opens correctly on microsoft excel. write.exprs(e,file = "mydata.csv", sep = ",", col.names = NA) here, e is an exprSet. notice i changed your "txt" to "csv"... i believe that by default, on msft windows, files ending in csv will automatically be opened by excel. also it better describes that this is a comma delimited flat file. hope this helps, rafael