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Alogmail2@aol.com
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Last seen 10.0 years ago
Hi Gordon,
Why creating ExpressionSet
>esetPROC = new("ExpressionSet", exprs = ddaux$G)
results in error if then running
>arrayQualityMetrics(expressionset=esetPROC,outdir ="esetPROC",force
=T)
?
Developers (Audrey Kauffmann and Wolfgang Huber) claim that
"expressionset is an object of class ExpressionSet for one color non
Affymetrix data"
(see definitions for prepdata() in their reference manual).
As to bg-correction: I agree that it makes sense usually.
I looked at the LIMMA user guide(11 November 2011): Agilent is
mentioned in
pp.16, 19, and 26 ...
and nothing special about one-color Agilent arrays.
But your read.maimages() is used in read.AgilentFE() from package
Agi4x44PreProcess to import Agilent one-color data sets as RGlist.
Thanks
Alex
In a message dated 6/9/2012 8:12:37 P.M. Pacific Daylight Time,
smyth@wehi.EDU.AU writes:
Hi Alex,
I don't know arrayQualityMetrics, but you are using the limma package
to
read single-channel Agilent data in a way that I think might cause
problems with down-stream analyses. Basically you're creating a two-
color
data object when your data is not actually of that type. This was a
time
when I suggested this sort of work-around as a stop-gap measure for
some
data problems, but hasn't been necessary for quite a few years.
I'd also recommend that you do some background correction. If I
understand your code correctly, I don't think it is currently making
use
of the background intensity column.
There is a case study in the limma User's Guide that deals with
single
channel Agilent data. Could you please have a read of that for a
cleaner
way to read Agilent data?
I don't know whether that will be enough to solve your
arrayQualityMetrics
problem, but perhaps it might.
Best wishes
Gordon
------------- original message -------------
[BioC] arrayQualityMetrics() doesn't work for one-color non Affy
arrays
Alogmail2 at aol.com Alogmail2 at aol.com
Fri Jun 8 09:39:21 CEST 2012
Dear List,
Could you share your experience with arrayQualityMetrics() for one-
color
non Affy arrays: it doesn't work for me (please see the code below).
Thanks
Alex Loguinov
UC, Berkeley
>options(error = recover, warn = 2)
>options(bitmapType = "cairo")
>.HaveDummy = !interactive()
> if(.HaveDummy) pdf("dummy.pdf")
>library("arrayQualityMetrics")
>head(targets)
FileName Treatment GErep Time Conc
T0-Control-Cu_61_new_252961010035_2_4
T0-Control-Cu_61_new_252961010035_2_4.txt C.t0.0 0 0 0
T0-Control-Cu_62_new_252961010036_2_1
T0-Control-Cu_62_new_252961010036_2_1.txt C.t0.0 0 0 0
T0-Control-Cu_64_252961010031_2_2
T0-Control-Cu_64_252961010031_2_2.txt C.t0.0 0 0 0
T0-Control-Cu_65_new_252961010037_2_2
T0-Control-Cu_65_new_252961010037_2_2.txt C.t0.0 0 0 0
T04h-Contr_06_new_252961010037_2_4
T04h-Contr_06_new_252961010037_2_4.txt C.t4.0 1 4 0
T04h-Contr_10_new_252961010035_1_2
T04h-Contr_10_new_252961010035_1_2.txt C.t4.0 1 4 0
> ddaux = read.maimages(files = targets$FileName, source =
"agilent",
other.columns = list(IsFound = "gIsFound", IsWellAboveBG =
"IsWellAboveBG",gIsPosAndSignif="gIsPosAndSignif",
IsSaturated = "gIsSaturated", IsFeatNonUnifOF = "gIsFeatNonUnifOL",
IsFeatPopnOL = "gIsFeatPopnOL", ChrCoord =
"chr_coord",Row="Row",Column="Col"),
columns = list(Rf = "gProcessedSignal", Gf = "gMeanSignal",
Rb = "gBGMedianSignal", Gb = "gBGUsed"), verbose = T,
sep = "\t", quote = "")
> class(ddaux)
[1] "RGList"
attr(,"package")
[1] "limma"
> names(ddaux)
[1] "R" "G" "Rb" "Gb" "targets" "genes"
"source"
"printer" "other"
I could apply:
>
> class(ddaux$G)
[1] "matrix"
>all(rownames(targets)==colnames(ddaux$G))
[1] TRUE
>esetPROC = new("ExpressionSet", exprs = ddaux$G)
But it results in errors:
>arrayQualityMetrics(expressionset=esetPROC,outdir ="esetPROC",force
=T)
The directory 'esetPROC' has been created.
Error: no function to return from, jumping to top level
Enter a frame number, or 0 to exit
1: arrayQualityMetrics(expressionset = esetPROC, outdir = "esetPROC",
force = T)
2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle =
reporttitle, outdir = outdir)
3: reportModule(p = p, module = modules[[i]], currentIndex =
currentIndex,
arrayTable = arrayTableCompact, outdir = outdir)
4: makePlot(module)
5: print(_x@plot_ (mailto:x@plot) )
6: print.trellis(_x@plot_ (mailto:x@plot) )
7: printFunction(x, ...)
8: tryCatch(checkArgsAndCall(panel, pargs), error = function(e)
panel.error(e))
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatchOne(expr, names, parentenv, handlers[[1]])
11: doTryCatch(return(expr), name, parentenv, handler)
12: checkArgsAndCall(panel, pargs)
13: do.call(FUN, args)
14: function (x, y = NULL, subscripts, groups, panel.groups =
"panel.xyplot", ..., col = "black", col.line = superpose.line$col,
col.symbol =
superpose.symb
15: .signalSimpleWarning("closing unused connection 5
(Report_for_exampleSet/index.html)", quote(NULL))
16: withRestarts({
17: withOneRestart(expr, restarts[[1]])
18: doWithOneRestart(return(expr), restart)
Selection: 0
Error in KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize =
nbin, :
(converted from warning) Binning grid too coarse for current (small)
bandwidth: consider increasing 'gridsize'
Enter a frame number, or 0 to exit
1: arrayQualityMetrics(expressionset = esetPROC, outdir = "esetPROC",
force = T)
2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle =
reporttitle, outdir = outdir)
3: reportModule(p = p, module = modules[[i]], currentIndex =
currentIndex,
arrayTable = arrayTableCompact, outdir = outdir)
4: makePlot(module)
5: do.call(_x@plot_ (mailto:x@plot) , args = list())
6: function ()
7: meanSdPlot(x$M, cex.axis = 0.9, ylab = "Standard deviation of the
intensities", xlab = "Rank(mean of intensities)")
8: meanSdPlot(x$M, cex.axis = 0.9, ylab = "Standard deviation of the
intensities", xlab = "Rank(mean of intensities)")
9: smoothScatter(res$px, res$py, xlab = xlab, ylab = ylab, ...)
10: grDevices:::.smoothScatterCalcDensity(x, nbin, bandwidth)
11: KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,
range.x
= range.x)
12: warning("Binning grid too coarse for current (small) bandwidth:
consider increasing 'gridsize'")
13: .signalSimpleWarning("Binning grid too coarse for current
(small)
bandwidth: consider increasing 'gridsize'",
quote(KernSmooth::bkde2D(x,
bandwidth = ba
14: withRestarts({
15: withOneRestart(expr, restarts[[1]])
16: doWithOneRestart(return(expr), restart)
Selection: 0
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] CCl4_1.0.11 vsn_3.22.0
arrayQualityMetrics_3.10.0 Agi4x44PreProcess_1.14.0
genefilter_1.36.0
[6] annotate_1.32.3 AnnotationDbi_1.16.19
limma_3.10.3
Biobase_2.14.0
loaded via a namespace (and not attached):
[1] affy_1.32.1 affyio_1.22.0 affyPLM_1.30.0
beadarray_2.4.2 BiocInstaller_1.2.1 Biostrings_2.22.0
[7] Cairo_1.5-1 cluster_1.14.2 colorspace_1.1-1
DBI_0.2-5 grid_2.14.2 Hmisc_3.9-3
[13] hwriter_1.3 IRanges_1.12.6 KernSmooth_2.23-7
lattice_0.20-6 latticeExtra_0.6-19 plyr_1.7.1
[19] preprocessCore_1.16.0 RColorBrewer_1.0-5 reshape2_1.2.1
RSQLite_0.11.1 setRNG_2011.11-2 splines_2.14.2
[25] stringr_0.6 survival_2.36-14 SVGAnnotation_0.9-0
tools_2.14.2 XML_3.9-4.1 xtable_1.7-0
[31] zlibbioc_1.0.1
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