[BioC] problems with readIllumina()

[Mark Dunning]

Hi Ina,

beadarray has changed a bit in the past two years. The readIllumina
function should be roughly the same. However it expects the contents
of the directory to be the output of Illumina's scanning software. For
instance, if there are files with the extension .txt other than the
bead-level files it could get confused easily. You can use the
sectionNames argument to readIllumina to specify which files to read
in.

Regards,

Mark

On Wed, Dec 15, 2010 at 11:25 PM, Ina Hoeschele <inah at vbi.vt.edu> wrote:
> Hi Karl and others,
>   I am getting the same error message with the readIllumina function and the new beadarray package:
>
>> setwd("C:/PHS_MESA_Epigenomics/5655508006")
>> BLData.normexp = readIllumina(singleChannel=TRUE, useImages=FALSE, illuminaAnnotation="Humanv4", normalizeMethod="none", backgroundMethod="normexp")
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") : cannot open file 'NA/NA': No such file or directory
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> 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 utils     datasets  methods   base
>
> other attached packages:
> [1] beadarray_2.0.2 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] limma_3.6.4  tools_2.12.0
>
>
> When I was working with similar data 2 years ago I had to specify the array names like this:
> readIllumina(textType=".txt",
>        arrayNames = c("4207121082_A_1","4207121082_A_2","4207121082_B_1",
>        "4207121082_B_2","4207121082_C_1","4207121082_C_2","4207121082_D_1",
>        "4207121082_D_2","4207121082_E_1","4207121082_E_2","4207121082_F_1",
>        "4207121082_F_2"), singleChannel=TRUE, useImages=FALSE,
>        normalizeMethod="none", backgroundMethod="normexp")
>
> Is this because I do not have a targets file? Do I get the error message because I did not specify the array names for 5655508006?
>
> Above, I am trying to read the data on a single chip (5655508006) - how can I read data on multiple chips (that are in different sub-directories (5655508006, 5655508014, etc.)) with one call to readIllumina?
>
> Many thanks for any help.
>
> Ina
>
> ----- Original Message -----
> From: "karl koechert" <karl.koechert at mdc-berlin.de>
> To: bioconductor at stat.math.ethz.ch
> Sent: Tuesday, November 2, 2010 10:13:15 AM
> Subject: [BioC] problems with readIllumina()
>
> Hey,
>
> I've been using beedarray quite often, but now with the new version I'm running in some error when trying to reading in the bead level data with readIllumina(). Does anyone know why this is happening or had a similar experience? What is meant with file 'NA/NA'?
>
> Thanks for any help!
> Karl
>
> see below:
>
>> bld=readIllumina(arrayNames=targets$Array, textType=".txt", backgroundMethod="none", annoPkg="Humanv4", useImages=FALSE)
> Fehler in file(file, "rt") : kann Verbindung nicht �ffnen //error: can't open connection
> Zus�tzlich: Warnmeldung: //additional: error
> In file(file, "rt") :
>  kann Datei 'NA/NA' nicht �ffnen: No such file or directory // can't open file 'NA/NA'
>> bld=readIllumina(useImages = FALSE, illuminaAnnotation = "Humanv4")
> Fehler in file(file, "rt") : kann Verbindung nicht �ffnen //error: can't open connection
> Zus�tzlich: Warnmeldung:
> In file(file, "rt") ://additional: error
>  kann Datei 'NA/NA' nicht �ffnen: No such file or directory // can't open file 'NA/NA'
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
> [4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] illuminaHumanv4BeadID.db_1.8.0 org.Hs.eg.db_2.4.6             RSQLite_0.9-2
> [4] DBI_0.2-5                      AnnotationDbi_1.12.0           limma_3.6.6
> [7] beadarray_2.0.1                Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.0
>
>
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>
>
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