Dear Gordon,
 
Thank you for the link to the newly updated  limma user guide and comments.
 
Best regards,
 
Alex
 
 
 
 
 
Alex Loguinov, Ph.D
Department of Nutritional Sciences
 and Toxicology
119 Morgan Hall,
University of California
Berkely, CA 94720 
 
 
In a message dated 6/13/2012 4:57:33 P.M. Pacific Daylight Time,  
smyth@wehi.EDU.AU writes:

Dear  Alex,

When I answer a question on the Bioconductor list, I am always  refering to 
current Bioconductor release unless stated otherwise.  I  don't think it is 
unreasonable to ask you to look at the current  documentation:

http://bioconductor.org/packages/2.10/bioc/vignettes/limma/inst/doc/usersgui
de.pdf

Please  send questions about arrayQualityMetrics to the authors of that  
package.

I'm not an author of the Agi4x44PreProcess package.   You could write to 
the authors and suggest they update the import  procedure.

Best  wishes
Gordon

---------------------------------------------
Professor  Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute  of Medical Research,
1G Royal Parade, Parkville, Vic 3052,  Australia.
http://www.statsci.org/smyth

On Wed, 13 Jun 2012,  Alogmail2@aol.com wrote:

> 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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