you can use the function RG.MA to convert your M and A values back into normalized R and G values. > RG.MA function (object) { object$R <- 2^(object$A + object$M/2) object$G <- 2^(object$A - object$M/2) object$M <- NULL object$A <- NULL new("RGList", unclass(object)) } Marcus >>> Jianping Jin <jjin at="" email.unc.edu=""> 2/08/2005 6:41:49 a.m. >>> 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 > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}

Thanks a lot Marcus! JP- --On Tuesday, August 02, 2005 11:19 AM +1200 Marcus Davy <mdavy at="" hortresearch.co.nz=""> wrote: > > you can use the function RG.MA to convert your M and A values back into > normalized R and G values. > >> RG.MA > function (object) > { > object$R <- 2^(object$A + object$M/2) > object$G <- 2^(object$A - object$M/2) > object$M <- NULL > object$A <- NULL > new("RGList", unclass(object)) > } > > Marcus > >>>> Jianping Jin <jjin at="" email.unc.edu=""> 2/08/2005 6:41:49 a.m. >>> > 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 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > ______________________________________________________ > > The contents of this e-mail are privileged and/or confidential to the > named recipient and are not to be used by any other person and/or > organisation. If you have received this e-mail in error, please notify > the sender and delete all material pertaining to this e-mail. > ______________________________________________________ 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