Pintilie, Melania
2004-Oct-25 20:53 UTC
[R] Question on bioconductor: reading affymetrix data
Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows:> d2=ReadAffy(widget=T)and I complete the fields as required. It does not complain. For example I could find the description:> description(d2)Experimenter name: BB Laboratory: FFL Contact information: Title: Heter URL: www.bioconductor.org A 1 word abstract is available. Use 'abstract' method. Information is available on: samples, preprocessing But if I want to see the values for MM I get an error:> mm(d2)[1:2]Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == "")) return(NULL) : missing value where TRUE/FALSE needed I appreciate any ideas you may have. Thank you. Melania Rm 15-433, ext 4886 Fax: (416) 946-2048
James MacDonald
2004-Oct-25 22:42 UTC
[R] Question on bioconductor: reading affymetrix data
This is a question that should be asked on the bioconductor mailing list
rather than R-help.
Quick answer:
library(reposTools)
install.packages2("whateverchiptypethisiscdf")
Where you have to replace whateverchiptypethisiscdf with e.g.,
hgu133acdf.
HTH,
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623>>> "Pintilie, Melania" <Melania.Pintilie@uhn.on.ca>
10/25/04 4:53 PM
>>>
Hi everyone,
My purpose is to read a .CEL file into R.
The .CEL file was created from a .CAB by using DTT software found on
Affymetrix website
I read the .CEL file in R using ReadAffy as follows:> d2=ReadAffy(widget=T)
and I complete the fields as required.
It does not complain. For example I could find the
description:> description(d2)
Experimenter name: BB
Laboratory: FFL
Contact information:
Title: Heter
URL: www.bioconductor.org
A 1 word abstract is available. Use 'abstract' method.
Information is available on: samples, preprocessing
But if I want to see the values for MM I get an error:
> mm(d2)[1:2]
Note: You did not specify a download type. Using a default value of:
Win32
This will be fine for almost all users
Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == ""))
return(NULL) :
missing value where TRUE/FALSE needed
I appreciate any ideas you may have. Thank you.
Melania
Rm 15-433, ext 4886
Fax: (416) 946-2048
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