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

[pcboutro at engmail.uwaterloo.ca]

Okay, that makes sense.  Just two more questions, then:
1. Do you have a guess-timate date for the next release?
2. Can I mix-and-match production/development modules, or will I need to 
download pretty much the whole development release to take advantage of changes 
in the affy package?

Thanks for the help,
Paul

Quoting Ben Bolstad <bolstad at stat.berkeley.edu>:

> 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
> > > 
> > 
> > 
> > 
> > 
> > ----------------------------------------
> > This mail sent through www.mywaterloo.ca
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> -- 
> Ben Bolstad <bolstad at stat.berkeley.edu>
> 




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