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@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@med.umich.edu<mailto:
>> jmacdon@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@stat.math.ethz.ch
>>        <mailto:Bioconductor@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]]

