Dear Jay, limma functions such a normalizeWithinArrays() and lmFit() all use spot weights automatically. As far as I know, maNorm() doesn't use spot weights. Best wishes Gordon > Date: Tue, 2 Jan 2007 14:51:17 -0700 > From: Jay Konieczka <jayk at="" u.arizona.edu=""> > Subject: [BioC] flagging spots in marray > To: bioconductor at stat.math.ethz.ch > Message-ID: <4C50AEE2-EBF6-4133-AF72-F6BE35FBE78E at u.arizona.edu> > Content-Type: text/plain > > Hi, > > I'm using the marray package to analyse my 2-color cDNA array data, > and I'm trying to sort out how to tell the various functions which > spots to use. I understand how to set the maSub vector in the layout > object, and my understanding is that the normalization functions will > then use this vector to know which spots to include in the > normalization procedures so long as subset=TRUE when I call a given > normalization function. But how do I flag spots within specific > arrays such that those spots will not be used in the normalization or > in the limma methods? For example, here is some code a friend of > mine was using to flag spots for normalization methods using the > limma function read.maimages(): > > #this function flags out bad spots defined as saturated, too small or > large, absent or manually flagged as bad. > filters <- function(x) { > okred <- x[,"F635 Mean"] < 65534 > okgreen <- x[,"F532 Mean"] < 65534 > fat <- x[,"Dia."] > 50 > skinny <- x[,"Dia."] < 150 > present <- x[,"Normalize"] < 1 > good <- x[,"Flags"] > -50.5 > as.numeric(okred & okgreen & fat & skinny & present & good) > } > > #read in data and gal file > RG = read.maimages(targets$FileName, source="genepix", > wt.fun=filters, other.columns=c("F635 SD", "B635 SD", "F532 SD", > "B532 SD", "F Pixels", "B Pixels", "B532 Mean","B635 Mean")) > > So now, because of the wt.fun parameter, those spots are considered > (or not) according to the filter function. What would be the > corresponding way to do this using marray? I'm assuming I must set > the name.W parameter when I call read.marrayRaw() to point to a > vector indicating the weights of each spot. If so, I can handle > this, but how do I ensure that the normalization methods will use > this vector? If the name.W parameter is set in the marrayRaw object, > will maNorm() know to use it by default? Or must I tell it that it > is set in some way? What about lmFit()? > > Thanks, > > Jay > > -- > Jay H. Konieczka > Ph.D. Student, Antin Lab > Molecular & Cellular Biology > University of Arizona > > Phone: 1.520.591.3446 > > 1656 E. Mabel, MRB 317 > Tucson, AZ 85724 USA > _____________________ > > > > [[alternative HTML version deleted]] > > > > ------------------------------ > > Message: 5 > Date: Wed, 03 Jan 2007 09:44:23 +1100 > From: Gordon Smyth <smyth at="" wehi.edu.au=""> > Subject: Re: [BioC] Plate or print-order effects - limma > To: Jenny Drnevich <drnevich at="" uiuc.edu=""> > Cc: bioconductor at stat.math.ethz.ch, J.delasHeras at ed.ac.uk, > Joao.Fadista at agrsci.dk > Message-ID: <6.2.5.6.1.20070103092525.02171590 at wehi.edu.au> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > At 07:38 AM 3/01/2007, Jenny Drnevich wrote: >>Hi Gordon, >> >>FYI - I was playing around with plotting print order effects, and >>found a discrepancy between the help documentation and the actual >>behavior of 'normalizeForPrintorder.rg '. The help file states "The >>function plotPrintorder or normalizeForPrintorder.rg with plot=TRUE >>returns no value but produces a plot as a side-effect." However, >>when I used 'normalizeForPrintorder.rg' with plot=TRUE, it not only >>produced the plot but spit out the entire list! > > You're right. I'll fix. > >>I'm using this function instead of the wrapper 'plotPrintorder' >>because I'm having trouble making the necessary layout list. I could >>only find a little bit of information about the layout list in >>'printorder' help page - is each component of the list (ngrid.r, >>ngrid.c, nspot.r and nspot.c) just a single number? In my case our >>printer has 48 tips and prints 12 x 4 blocks of 420 spots, one dip >>per spot, so would my layout just be a list of ngrid.r = 12, ngrid.c >>= 4, nspot.r = 420, and nspot.c = 1? > > You also need to know the number of rows (nspot.r) and columns > (nspot.c) of spots in each block. nspot.c is almost certainly greater than 1. > > You also need to check with your microarray printing unit whether > printing of your arrays begins in the top right or top left of each > block, and whether it proceeds by rows or columns. The default for > normalizeForPrintorder assumes topleft by rows, which the usual setup > at UCSF. But the AGRF in Australia uses topright by rows. > > See help("PrinterLayout-class"). The read.maimages() function > produces the printer layout information automatically as RG$printer > for some input sources including GenePix and ImageGene. > > Best wishes > Gordon > >>Thanks, >>Jenny >> >> > sessionInfo() >>R version 2.4.0 (2006-10-03) >>i386-pc-mingw32 >> >>locale: >>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>States.1252;LC_MONETARY=English_United >>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >>attached base packages: >>[1] "splines" "tools" "methods" "stats" "graphics" "grDevices" >>[7] "utils" "datasets" "base" >> >>other attached packages: >> affyQCReport simpleaffy made4 scatterplot3d ade4 >> "1.12.0" "2.8.0" "1.8.0" "0.3-24" "1.4-2" >> affyPLM affydata affycoretools annaffy xtable >> "1.10.0" "1.10.0" "1.7.5" "1.6.0" "1.4-2" >> gcrma matchprobes biomaRt RCurl XML >> "2.6.0" "1.6.0" "1.8.0" "0.7-0" "1.2-0" >> GOstats Category genefilter survival KEGG >> "2.0.3" "2.0.3" "1.12.0" "2.29" "1.14.1" >> RBGL annotate GO graph limma >> "1.10.0" "1.12.0" "1.14.1" "1.12.0" "2.9.1" >> affy affyio Biobase RWinEdt >> "1.12.1" "1.2.0" "1.12.2" "1.7-5" >> >>Jenny Drnevich, Ph.D. >> >>Functional Genomics Bioinformatics Specialist >>W.M. Keck Center for Comparative and Functional Genomics >>Roy J. Carver Biotechnology Center >>University of Illinois, Urbana-Champaign >> >>330 ERML >>1201 W. Gregory Dr. >>Urbana, IL 61801 >>USA >> >>ph: 217-244-7355 >>fax: 217-265-5066 >>e-mail: drnevich at uiuc.edu > > > > ------------------------------ > > Message: 6 > Date: Wed, 03 Jan 2007 10:55:27 +0000 > From: Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> > Subject: [BioC] Import GEO Soft format > To: bioconductor at stat.math.ethz.ch > Message-ID: <459B8B9F.4060105 at icr.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > I have got some aCGH data from GEO, what is the best way to get this > into R in a suitable object. Is there a package that interprets Soft > format or is the approach to produce tab-delimited files? > > Thanks > > -- > ************************************************************** > > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > MUCRC > 15 Cotswold Road > Sutton, Surrey SM2 5NG > United Kingdom > > Tel: +44 (0) 20 8722 4109 > Fax: +44 (0) 20 8722 4141 > > Email: daniel.brewer at icr.ac.uk > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 47, Issue 2 > ******************************************* >