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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > 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 > 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

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 >>>>> >>>>>_______________________________________________ >>>>>Bioconductor mailing list >>>>>Bioconductor at stat.math.ethz.ch >>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >>>>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 >>> >>> >>> >>>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 > > > > 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