[BioC] problems with readIllumina() for many BeadChips
Ina Hoeschele
inah at vbi.vt.edu
Tue Feb 15 23:05:57 CET 2011
Hi Mark et al.,
I still have issues reading data from multiple BeadChips using readIllumina (same as below). My BeadChip is HumanHT-12 v4 Expression BeadChip
My data are in 8 directories, corresponding to 8 chips, containing only Beadscan output (no other txt files). In each directory, there is one "SQL server compact edition database file", and for each of the sections A through L, there is a Microsoft Office Excel comma separated values file, a Text document, an IDAT file, a LOCS file, a TIFF image and an XML document. There are NO other files except for 3 files whose names end in _fiducial #1_Red_center, _fiducial #2_Red_center, and _fiducial #3_Red_center.
I have been able to read the data into R with readIllumina using this code:
setwd("C:/PHS_MESA_Epigenomics/5655508006")
BLData = readIllumina(useImages=FALSE, illuminaAnnotation="Humanv4",
sectionNames=c("5655508006_A","5655508006_B","5655508006_C","5655508006_D","5655508006_E","5655508006_F","5655508006_G","5655508006_H","5655508006_I","5655508006_J","5655508006_K","5655508006_L"))
Question 1: if I use the same code but omit sectionNames, then it does not read the data. I will have to deal with hundred(s) of BeadChips and so specifying sectionNames for each chip is awkward. Why does nit not automatically find all 12 txt files? Moreover, currently I read the data from each directory (= BeadChip) separately - that would be hundred(s) read statements - is there a way to get readIllumina to read all txt files in ALL subdirectories with a single call to readIllumina?
Question 2: this is about the arguments to readIllumina. The arguments as described in the beadarray manual are: dir, useImages, illuminaAnnotation, sectionNames and metricsFile. Then it states "other argumdents to pass when reading bead-level text files". What are these other arguments, where are they described, are they important (does one have to look at the source code to find out??) In the old version of the beadarray package, I used additional arguments that seem to no longer work and are no longer described, for example textType, singleChannel, normalizeMethod, backgroundMethod. When I include some of these old arguments, readIllumina fails.
Here is the error message that I get when I try to read the data in one directory without specifying sectionNames:
> setwd("C:/PHS_MESA_Epigenomics/5655508006")
> BLData = readIllumina(useImages=FALSE, illuminaAnnotation="Humanv4")
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 2.12.1 (2010-12-16)
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] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] preprocessCore_1.12.0 geneplotter_1.28.0 lattice_0.19-13
[4] annotate_1.28.0 AnnotationDbi_1.12.0 RColorBrewer_1.0-2
[7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1
[10] gdata_2.8.1 gtools_2.6.2 beadarray_2.0.3
[13] Biobase_2.10.0
loaded via a namespace (and not attached):
[1] DBI_0.2-5 limma_3.6.9 RSQLite_0.9-4 xtable_1.5-6
Many thanks for your time and help.
Ina
----- Original Message -----
From: "Mark Dunning" <mark.dunning at gmail.com>
To: "Ina Hoeschele" <inah at vbi.vt.edu>
Cc: bioconductor at stat.math.ethz.ch
Sent: Monday, December 20, 2010 6:02:12 AM
Subject: Re: [BioC] problems with readIllumina()
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
>
>
> [[alternative HTML version deleted]]
>
>
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