Thanks Gordon and Naomi for your time and efforts to help me out. The the code worked well for me. One more question. What if I wanted to get the loess normalized expression values in addition to M & As? Can I extract the expression values from after normalizeWithinArrays or do I have to use something like "loessFit"? best regards! JP- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin at email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --On Saturday, July 30, 2005 11:55 PM +1000 Gordon Smyth <smyth at="" wehi.edu.au=""> wrote: > As you've deduced, the problem is that your arrays do not a constant > block size. limma assumes a constant block size for > normalizeWithinArrays() and imageplot(). > > Here is a work-around for GenePix data: > > for (b in 1:48) { > i <- RG$genes$Block==b > MA2 <- normalizeWithinArrays(RG[i,],method="loess") > if(b==1) > MA <- MA2 > else > MA <- rbind(MA,MA2) > } > > This will perform print-tip-loess normalization even though there are > irregular numbers of spots in the print-tip groups. > > Gordon > >> Date: Fri, 29 Jul 2005 16:42:58 -0400 >> From: Naomi Altman <naomi at="" stat.psu.edu=""> >> Subject: Re: [BioC] limma error message >> To: Jianping Jin <jjin at="" email.unc.edu=""> >> Cc: Bioconductor at stat.math.ethz.ch >> Message-ID: <6.2.1.2.2.20050729163707.040c3240 at imap.stat.psu.edu> >> Content-Type: text/plain; charset="us-ascii"; format=flowed >> >> 28*28*12*4 >> [1] 37632 >> >> But you have 34970 genes. >> >> The simplest thing to do is to add the missing lines to your GPR files. >> >> You could probably do this in your favorite text manipulation language >> but with 8 arrays, you might be able to do it manually more quickly. >> >> --Naomi >> >> >> At 12:13 PM 7/29/2005, Jianping Jin wrote: >> > Dear Naomi and BioConductor list, >> > >> > Thanks for your kind reply! But I got the same error message after >> > re-run the program as the following: >> > >> >> targets <- readTargets() >> >> RG <- read.maimages(targets$FileName, source="genepix") >> > Read 0341_3289_A5_052_HO34K_sample-1_HRef_scan2.gpr >> > Read 0341_3290_A5_053_HO34K_sample-2_HRef_scan2.gpr >> > Read 0341_3291_A5_054_HO34K_sample-3_HRef.gpr >> > Read 0341_3292_A5_055_HO34K_sample-4_HRef.gpr >> > Read 0341_3293_A5_056_HO34K_sample-5_HRef.gpr >> > Read 0341_3294_A5_057_HO34K_sample-6_HRef.gpr >> > Read 0341_3295_A5_058_HO34K_sample-7_HRef.gpr >> > Read 0341_3296_A5_059_HO34K_sample-8_HRef.gpr >> >> summary(RG) >> > Length Class Mode >> > R 279760 -none- numeric >> > G 279760 -none- numeric >> > Rb 279760 -none- numeric >> > Gb 279760 -none- numeric >> > targets 1 data.frame list >> > genes 5 data.frame list >> > >> >> dim(RG) >> > [1] 34970 8 >> > >> >> getLayout(RG$genes) >> > $ngrid.r >> > [1] 12 >> > >> > $ngrid.c >> > [1] 4 >> > >> > $nspot.r >> > [1] 28 >> > >> > $nspot.c >> > [1] 28 >> > >> > attr(,"class") >> > [1] "PrintLayout" >> > >> >> MA <- normalizeWithinArrays(RG, layout=list(ngrid.r=12, ngrid.c=4, >> > nspot.r=28, nspot.c=28)) >> > Error: subscript out of bounds >> > >> > I checked the data files and found nsopt.r and nspot.c in the last one >> > third blocks of every files were changed from 28 to 24 and 23 >> > respectively. That may be the reason for the error message. Do you have >> > any ways to handle this? >> > >> > Many thanks! >> > >> > JP- >> > >> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> > x Jianping Jin Ph.D. x >> > x Bioinformatics scientist x >> > x Center for bioinformatics x >> > x 3133 Bioinformatics Building x >> > x CB# 7104 x >> > x University of North Carolina x >> > x Chapel Hill, NC 27599 x >> > x Tel: (919)843-6105 x >> > x Fax: (919)843-3103 x >> > x E-mail: jjin at email.unc.edu x >> > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> > >> > --On Thursday, July 28, 2005 5:17 PM -0400 Naomi Altman >> > <naomi at="" stat.psu.edu=""> wrote: >> > >> >> layout=list(ngrid.r= ,ngrid.c= ,nspot.r= , nspot.c= ) >> >> >> >> Your array is laid out in blocks according to the print tip >> >> configuration of the printer. >> >> nspot.r is the number of rows in each block >> >> nspot.c is the number of columns in each block >> >> >> >> ngrid.r is the number of rows of blocks >> >> ngrid.c is the number of columns of blocks >> >> >> >> e.g. a typical 8 tip design might have 4 rows and 2 columns of blocks >> >> >> >> If you don't know the right numbers to put in, look at the raw data - >> >> the block number and row and column are output to your expression >> >> file. >> >> >> >> --Naomi >> >> >> >> At 04:49 PM 7/28/2005, you wrote: >> >>> Thanks Naomi! Could you explain how to specify parameter "layout"? >> >>> JP- >> >>> >> >>> --On Thursday, July 28, 2005 3:35 PM -0400 Naomi Altman >> >>> <naomi at="" stat.psu.edu=""> wrote: >> >>> >> >>>> I got this message when I used the wrong layout file. >> >>>> >> >>>> --Naomi >> >>>> >> >>>> At 03:03 PM 7/28/2005, Jianping Jin wrote: >> >>>>> Dear BioConductor list, >> >>>>> >> >>>>> I got an error, Error: subscipt out of bounds, when I started to >> >>>>> run a limma program normalizeWithinArrays(). What I wanted to do >> >>>>> was to normalize eight cDNA slides. >dim(RG): 34970 8. >> >>>>> >> >>>>> I used >debug(normalizeWithinArrays) and then >> >>>>> > normalizeWithinArrays(RG) to debug by either Browse[1]> n or c as >> >>>>> well. But when I retried the program it gave me the same error >> >>>>> message above. >> >>>>> >> >>>>> I will highly appreciate it if any one could give it shot. >> >>>>> >> >>>>> >> >>>>> Best regards! >> >>>>> >> >>>>> JP- >> >>>>> >> >>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> >>>>> x Jianping Jin Ph.D. x >> >>>>> x Bioinformatics scientist x >> >>>>> x Center for bioinformatics x >> >>>>> x 3133 Bioinformatics Building x >> >>>>> x CB# 7104 x >> >>>>> x University of North Carolina x >> >>>>> x Chapel Hill, NC 27599 x >> >>>>> x Tel: (919)843-6105 x >> >>>>> x Fax: (919)843-3103 x >> >>>>> x E-mail: jjin at email.unc.edu x >> >>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> >>>>> >> >>>> >> >>>> Naomi S. Altman 814-865-3791 (voice) >> >>>> Associate Professor >> >>>> Bioinformatics Consulting Center >> >>>> Dept. of Statistics 814-863-7114 (fax) >> >>>> Penn State University 814-865-1348 >> >>>> (Statistics) University Park, PA 16802-2111 >