[BioC] Help regarding mas5 normalization

[James W. MacDonald]

Nayeem Quayum wrote:
> Hello everybody,
> I am trying to use mas5 to normalize some array data and using mas5 and
> mas5calls. But I received these warning message. If anybody can explain the
> problem I would really appreciate that. Thanks in advance.
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...Warning message:
> 'loadURL' is deprecated.
> Use 'load(url())' instead.
> See help("Deprecated")
> Warning message:
> 'loadURL' is deprecated.
> Use 'load(url())' instead.
> See help("Deprecated")
> Warning message:
> 'loadURL' is deprecated.
> Use 'load(url())' instead.
> See help("Deprecated")
> There were 14 warnings (use warnings() to see them)
> Note: http://www.bioconductor.org/repository/devel/package/Win32 does not
> seem to have a valid repository, skipping
> Note: You did not specify a download type. Using a default value of: Source
> This will be fine for almost all users
> 
> Error in FUN(X[[1]], ...) : no slot of name "Uses" for this object of class
> "localPkg"

As Adai already noted, a sessionInfo() would be very helpful here. 
However, these sort of errors usually indicate incompatible BioC 
packages. A reasonable thing to do to fix this would be to get the 
latest version of R and then re-install BioC using the biocLite() script 
that can be sourced into R by

source("http://www.bioconductor.org/biocLite.R")
biocLite()

Best,

Jim


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-- 
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