[BioC] problem with justRMA in 2.10.0
James W. MacDonald
jmacdon at med.umich.edu
Mon Nov 9 21:00:18 CET 2009
What do you get from
affyio:::read.celfile.header(list.celfiles()[1], info = "full")
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()
> [[1]]
> character(0)
>
> [[2]]
> character(0)
>
> [[3]]
> character(0)
>
> [[4]]
> character(0)
>
> [[5]]
> character(0)
>
> [[6]]
> character(0)
>
> [[7]]
> character(0)
>
> [[8]]
> character(0)
>
> [[9]]
> character(0)
>
> [[10]]
> character(0)
>
> [[11]]
> character(0)
>
> [[12]]
> character(0)
>
> [[13]]
> character(0)
>
> [[14]]
> character(0)
>
> [[15]]
> character(0)
>
> [[16]]
> character(0)
>
> [[17]]
> character(0)
>
> [[18]]
> character(0)
>
> [[19]]
> character(0)
>
> [[20]]
> character(0)
>
> [[21]]
> character(0)
>
> [[22]]
> character(0)
>
> [[23]]
> character(0)
>
> [[24]]
> character(0)
>
> [[25]]
> character(0)
>
> [[26]]
> character(0)
>
> [[27]]
> character(0)
>
> [[28]]
> character(0)
>
> [[29]]
> character(0)
>
> [[30]]
> character(0)
>
> [[31]]
> character(0)
>
> [[32]]
> character(0)
>
> [[33]]
> character(0)
>
> [[34]]
> character(0)
>
> [[35]]
> character(0)
>
> [[36]]
> character(0)
>
> [[37]]
> character(0)
>
> [[38]]
> character(0)
>
> [[39]]
> character(0)
>
> [[40]]
> character(0)
>
> [[41]]
> character(0)
>
> [[42]]
> character(0)
>
> [[43]]
> character(0)
>
> [[44]]
> character(0)
>
> [[45]]
> character(0)
>
> [[46]]
> character(0)
>
> [[47]]
> character(0)
>
> [[48]]
> character(0)
>
> [[49]]
> character(0)
>
> [[50]]
> character(0)
>
> [[51]]
> character(0)
>
> [[52]]
> character(0)
>
> [[53]]
> character(0)
>
> [[54]]
> character(0)
>
> [[55]]
> character(0)
>
> [[56]]
> character(0)
>
> [[57]]
> character(0)
>
> [[58]]
> character(0)
>
> [[59]]
> character(0)
>
> [[60]]
> character(0)
>
> [[61]]
> character(0)
>
> [[62]]
> character(0)
>
> [[63]]
> character(0)
>
> [[64]]
> character(0)
>
> [[65]]
> character(0)
>
> [[66]]
> character(0)
>
> [[67]]
> character(0)
>
> [[68]]
> character(0)
>
> [[69]]
> character(0)
>
>
> On Mon, Nov 9, 2009 at 2:24 PM, James W. MacDonald
> <jmacdon at med.umich.edu <mailto: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>
> <mailto: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>
> <mailto: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
>
>
--
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
More information about the Bioconductor
mailing list