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

[pcboutro at engmail.uwaterloo.ca]

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
> 
> 
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