[BioC] Re: Warnings with Affy R 1.7.0 (Continued)

[Ben Bolstad]

These warnings have been eliminated in the current development affy
packages. You will likely get a lot of these type of warnings when you
use the 1.1 release affy package with R 1.7.0

Thanks,

Ben






> Hi again all,
> 
> The warnings I detailed below continue with every command I run after reading 
> in Cel files via ReadAffy.  In addition, I get an error with:
> 
> > Data2 <- ReadAffy();
> Warning message: 
> the condition has length > 1 and only the first element will be used in: if (dim
> (intensity(cel)) != dim.intensity) stop(paste("CEL file dimension mismatch !\n
> (file",  
> 
> > nData2 <- normalize(Data, method="loess");
> Error: couldn't find function "predict.loess"
> In addition: There were 50 or more warnings (use warnings() to see the first 50)
> 
> > traceback();
> 6: normalize.loess(intensity(abatch)[Index, ], ...)
> 5: normalize.AffyBatch.loess(object, ...)
> 4: do.call(method, alist(object, ...))
> 3: .local(object, ...)
> 2: normalize(Data, method = "loess")
> 1: normalize(Data, method = "loess")
> 
> When I ?predict.loess I find it is in the modreg package, which appears to be 
> already loaded.  Nevertheless, preceding the above commands with
> > library(modreg);
> 
> Gives the same error message.
> Paul
> 
> Quoting pcboutro at engmail.uwaterloo.ca:
> 
> > Hi all,
> > 
> > I was just testing out the affy package with a pair RG-U34A chips.  I get a 
> > series of warnings when using the package, and I can't figure if these are 
> > something I should be concerned about.  I should also note that I installed R
> > 
> > 1.7.0 today and removed my old 1.6.2: not sure if that would make a 
> > difference.  The warnings are all identical, so I only show the first few
> > below.
> > 
> > Is this something to be concerned about, or can I safely ignore it?  Any 
> > comments appreciated,
> > Paul
> > 
> > 
> > > dir();
> > [1] "U34A_100402_IM01T_LH.CEL" "U34A_100402_IM02T_LH.CEL"
> > 
> > > Data <- ReadAffy();
> > Warning message: 
> > the condition has length > 1 and only the first element will be used in: if
> > (dim
> > (intensity(cel)) != dim.intensity) stop(paste("CEL file dimension mismatch
> > !\n
> > (file", 
> > 
> > > eset <- rma(Data);
> > There were 50 or more warnings (use warnings() to see the first 50)
> > > warnings();
> > Warning messages:
> > 1: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 2: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 3: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 4: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 5: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 6: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 7: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 8: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 9: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next 
> > 10: the condition has length > 1 and only the first element will be used in:
> > if 
> > (is.na(ans[[i]])) next
> > 
> > 
> > ----------------------------------------
> > This mail sent through www.mywaterloo.ca
> > 
> 
> 
> 
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>