[BioC] Regarding GCRMA normalisation

[James W. MacDonald]

Hi Sneha,

sneha patil wrote:
> hiii,
> Myself Sneha...
> I want to discuss the error am repeatedly getting while running the GCRMA
> normalization and cannot solve it.Ihave installed the required HG_U95Av2
> probes and CDF packages still it is giving this error.Can u please help me.
> 
> 
>> library(gcrma)
>> esetGCRMA <- gcrma(rawdata)
> Adjusting for optical effect.........Done.
> Computing affinitiesError in getProbePackage(probepackagename) :
>   The current operation could not access the Bioconductor repository. Please
> check your internet connection, and report further problems to
> bioconductor at stat.math.ethz.ch
> 

What we need here is the output from sessionInfo() (note the two 
parentheses). What you have given is just the function itself.

And you could also give us the output from typing

rawdata

at the R prompt as well (after creating the AffyBatch you are calling 
'rawdata').

Best,

Jim


>> sessionInfo
> function (package = NULL)
> {
>     z <- list()
>     z$R.version <- R.Version()
>     z$locale <- Sys.getlocale()
>     if (is.null(package)) {
>         package <- grep("^package:", search(), value = TRUE)
>         keep <- sapply(package, function(x) x == "package:base" ||
>             !is.null(attr(as.environment(x), "path")))
>         package <- sub("^package:", "", package[keep])
>     }
>     pkgDesc <- lapply(package, packageDescription)
>     if (length(package) == 0)
>         stop("no valid packages were specified")
>     basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) &&
>         x$Priority == "base")
>     z$basePkgs <- package[basePkgs]
>     if (any(!basePkgs)) {
>         z$otherPkgs <- pkgDesc[!basePkgs]
>         names(z$otherPkgs) <- package[!basePkgs]
>     }
>     loadedOnly <- loadedNamespaces()
>     loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
>     if (length(loadedOnly)) {
>         names(loadedOnly) <- loadedOnly
>         pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
>         z$loadedOnly <- pkgDesc[loadedOnly]
>     }
>     class(z) <- "sessionInfo"
>     z
> }
> <environment: namespace:utils>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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