Entering edit mode
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@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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