[BioC] problem with justRMA in 2.10.0

[James W. MacDonald]

Joseph Dougherty wrote:
>  > sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] gcrma_2.18.0  affy_1.24.1   Biobase_2.6.0
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        Biostrings_2.14.2    IRanges_1.4.4
> [4] preprocessCore_1.8.0 splines_2.10.0       tools_2
> 
> The only difference I see is we don't have the patched R 2.10.0.  Is 
> that the dev version?

No, the dev version is R-devel. R-patched is what will be released as 
R-2.10.1 in a month or so.

So it looks like there isn't a mis-matched package here. As of BioC 2.5 
we now add scan date information to the AffyBatch, so there are actually 
two AnnotatedDataFrames being produced. I am betting that the problem is 
arising when the scan data are put into an AnnotateDataFrame.

What do you get if you run the following two functions in the directory 
that contain your celfiles?

fakePheno <- function(){
filenames <- list.celfiles()
samplenames <- sub("^/?([^/]*/)*", "", filenames)
         pdata <- data.frame(sample = seq_len(length(filenames)), 
row.names = samplenames)
         phenoData <- new("AnnotatedDataFrame", data = pdata,
             varMetadata = data.frame(labelDescription = "arbitrary 
numbering",
                 row.names = "sample"))
pData(phenoData)
}

fakeScan <- function(){
filenames <- list.celfiles()
scandates <- sapply(seq_len(length(filenames)), function(x) {
sdate <- affyio:::read.celfile.header(filenames[x], info = 
"full")[["ScanDate"]]
if(is.null(sdate))
NA_character_
else
sdate
})
scandates
}

Best,

Jim



> 
> Thanks,
> Joe
> 
> 
> On Mon, Nov 9, 2009 at 9:25 AM, James W. MacDonald 
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>> wrote:
> 
>     Hi Joseph,
> 
> 
>     Joseph Dougherty wrote:
> 
>         Hello,
> 
>         Has this bug been resolved?  I am working in R 2.10 for the
>         first time (also
>         a on a new linux server) and I am getting a strange error with
>         ReadAffy().
>         I don't have this error on my Windows machine, or our old
>         server, which are
>         still on earlier versions of R.
> 
> 
>     The bug in justRMA() didn't affect ReadAffy().
> 
> 
>             dat<-ReadAffy()
> 
>         Error in value[[3L]](cond) :
>          row names supplied are of the wrong length
>          AnnotatedDataFrame 'initialize' could not update varMetadata:
>          perhaps pData and varMetadata are inconsistent?
> 
>         I am just trying to load all of the Cel files in a directory.  I
>         get the
>         same message without a phenoData file (the way I usually run
>         it), or if I
>         make a simple one, which suggests to me this error message is
>         probably not
>         germane.     This could also be some other problem with the new
>         server or
>         the R install, but since Frasier had a similar error message, I
>         thought I
>         would check with you all first, before trying to make guess on
>         what else
>         could be going on.  I first got the error on Thursday.  I
>         deleted and
>         re-installed by bioconductor libraries tonight and stil get the
>         error.
> 
> 
>     You always need to supply us with your sessionInfo(). I get this to
>     work with a new version of R, so it is likely you have mis-matched
>     packages.
> 
>      > dat <- ReadAffy()
>      > sessionInfo()
>     R version 2.10.0 Patched (2009-11-05 r50317)
>     i386-pc-mingw32
> 
>     locale:
>     [1] LC_COLLATE=English_United States.1252
>     [2] LC_CTYPE=English_United States.1252
>     [3] LC_MONETARY=English_United States.1252
>     [4] LC_NUMERIC=C
>     [5] LC_TIME=English_United States.1252
> 
>     attached base packages:
>     [1] stats     graphics  grDevices datasets  utils     methods   base
> 
>     other attached packages:
>     [1] affy_1.24.1   Biobase_2.6.0
> 
>     loaded via a namespace (and not attached):
>     [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.0
> 
>     Best,
> 
>     Jim
> 
> 
> 
>         Thanks,
> 
>         Joe Dougherty
> 
>                [[alternative HTML version deleted]]
> 
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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
> 
> 

-- 
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