[BioC] problem with justRMA in 2.10.0

James W. MacDonald jmacdon at med.umich.edu
Mon Nov 9 22:12:31 CET 2009


This has been fixed in both the devel (1.25.2) and release (1.24.2) 
versions of affy. You can either wait for it to propagate through the 
build system (1-2 days) or get it from svn.

Best,

Jim



Joseph Dougherty wrote:
> fakescan seems to have a problem perhaps:
> 
>> fakePheno()
>                   sample
> Normal_A10.CEL         1
> Normal_C06.CEL         2
> Normal_C07.CEL         3
> Normal_C08.CEL         4
> Normal_C09.CEL         5
> Normal_C10.CEL         6
> Normal_C11.CEL         7
> Normal_D01.CEL         8
> Normal_D02.CEL         9
> Normal_D03.CEL        10
> Tumor7011_A05.CEL     11
> Tumor7011_C07.CEL     12
> Tumor7011_E05.CEL     13
> Tumor7011_F05.CEL     14
> Tumor7989_A10.CEL     15
> Tumor7989_B08.CEL     16
> Tumor7989_C09.CEL     17
> Tumor7989_C10.CEL     18
> Tumor7989_D10.CEL     19
> Tumor7989_F08.CEL     20
> Tumor7989_F09.CEL     21
> Tumor7989_G09.CEL     22
> Tumor7989_G10.CEL     23
> Tumor7989_H03.CEL     24
> Tumor7989_H09.CEL     25
> Tumor7996_B03.CEL     26
> Tumor7996_B06.CEL     27
> Tumor7996_D06.CEL     28
> Tumor7996_F06.CEL     29
> Tumor8340_A02.CEL     30
> Tumor8340_A03.CEL     31
> Tumor8340_A04.CEL     32
> Tumor8340_A09.CEL     33
> Tumor8340_A10.CEL     34
> Tumor8340_B07.CEL     35
> Tumor8340_B08.CEL     36
> Tumor8340_B09.CEL     37
> Tumor8340_B11.CEL     38
> Tumor8340_B12.CEL     39
> Tumor8340_C05.CEL     40
> Tumor8340_C06.CEL     41
> Tumor8340_C07.CEL     42
> Tumor8340_C08.CEL     43
> Tumor8340_C09.CEL     44
> Tumor8340_D01.CEL     45
> Tumor8340_E03.CEL     46
> Tumor8340_E08.CEL     47
> Tumor8340_F03.CEL     48
> Tumor8340_F07.CEL     49
> Tumor8461_A02.CEL     50
> Tumor8461_C01.CEL     51
> Tumor8461_C06.CEL     52
> Tumor8461_C12.CEL     53
> Tumor8615_A05.CEL     54
> Tumor8615_A06.CEL     55
> Tumor8615_A07.CEL     56
> Tumor8615_A10.CEL     57
> Tumor8615_B01.CEL     58
> Tumor8615_B08.CEL     59
> Tumor8615_B10.CEL     60
> Tumor8615_C01.CEL     61
> Tumor8615_C02.CEL     62
> Tumor8615_C08.CEL     63
> Tumor8615_C10.CEL     64
> Tumor8615_E07.CEL     65
> Tumor8615_F01.CEL     66
> Tumor8615_F03.CEL     67
> Tumor8615_F07.CEL     68
> Tumor8615_H09.CEL     69
> 
>> fakeScan()
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> 
> On Mon, Nov 9, 2009 at 2:24 PM, James W. MacDonald <jmacdon at med.umich.edu>wrote:
> 
>>
>> 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]]
>>>
>>>        _______________________________________________
>>>        Bioconductor mailing list
>>>        Bioconductor at stat.math.ethz.ch
>>>        <mailto:Bioconductor at stat.math.ethz.ch>
>>>
>>>        https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>        Search the archives:
>>>        http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>    --    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
>>
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
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> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
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



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