[BioC] normalizing incomplete arrays [was: limma errormessage]
Jianping Jin
jjin at email.unc.edu
Tue Aug 2 16:04:58 CEST 2005
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
>>
>
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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
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