[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]]
>
> _______________________________________________
> Bioconductor mailing list
> 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
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