[R] Normalization problem

From: Nayeem Quayum <nayeemquayum_at_gmail.com>
Date: Wed 26 Jul 2006 - 08:27:02 EST


At first I would like to express the gratitude toward Oosting, J. and James MacDonal for their help solving the previous problem I posted on this forum. Now I have a new problem. I was trying to normalize set of microarray data on HGU133 paltform. I put all the HGU133A platform chips in one directory and all the other HGU133B chips on another directory. When I tried to normalized them using same script HGU133A data worked fine but got error for HGU133B platform data. The code is

library(affy)
Data <- ReadAffy()
eset <- mas5(Data)
Calls <-mas5calls(Data)

The errors I got are:

background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...Warning message: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping
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 11 warnings (use warnings() to see them) Note: http://www.bioconductor.org/repository/devel/package/Source does not seem to have a valid repository, skipping Warning message:
cannot open: HTTP status was '403 Forbidden' 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"

Thanks in advance for your help.

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