hi,
In the package Agi4x44PreProcess I took the expression value as
*MeanSigna*l,
then by the method *BGandNorm,* the background subtraction and the
normalization between the array is done.But the array should be
normalized
within the array also first.This the script what is given in
Agi4x44PreProcess for normalization.I didnt find any option for within
the
array normalization.
> ddNORM = BGandNorm(dd, BGmethod = "half", NORMmethod = "quantile",
+ foreground = "MeanSignal", background = "BGMedianSignal",
+ offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE)
please help me out how can we do the normalization within the array
before
between the array normalization for one color agilent array.
thank you.
[[alternative HTML version deleted]]
On Fri, Feb 19, 2010 at 1:29 AM, neeraj rana <kushrn at="" gmail.com="">
wrote:
> hi,
>
> In the package Agi4x44PreProcess ?I took the expression value as
*MeanSigna*l,
> then by the method *BGandNorm,* the background subtraction and the
> normalization between the array is done.But the array should be
normalized
> within the array also first.This the script what is given in
> Agi4x44PreProcess for normalization.I didnt find any option for
within the
> array normalization.
>
>> ddNORM = BGandNorm(dd, BGmethod = "half", NORMmethod = "quantile",
> + foreground = "MeanSignal", background = "BGMedianSignal",
> + offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE)
>
> please help me out how can we do the normalization within the array
before
> between the array normalization for one color agilent array.
For one-color arrays, it usually suffices to perform between-array
normalization.
Sean
Hi all,
I am trying to read and visualize data obtained from an agilent chip.
For this purpose I use limma package and the read.maimages function as
follows
fileRG.raw <- read.maimages("File",source="agilent")
FileRG gets read correctly. When I check the dimensions it shows to
have
243494 probes which seem to be correctly annotated. I, then attach the
layout for the chip from the GAL file:
galinfo <- readGAL(fileGAL)
fileRG.raw$printer<-getLayout(galinfo)
and try to plot R/G according to this prnter layout:
imageplot(log2(fileRG.raw$R),fileRG.raw$printer,zlim=c(0,9),main="R-Fo
r.RAW")
However, I obtain the following error:
> Error in imageplot(log2(fileRG.raw$R), fileRG.raw$printer, zlim =
c(0, :
> Number of image spots does not agree with layout dimensions
Which is due to the fact that the gal file has 912*267 dimension
corresponding to 243504 probes. Checking the expression raw
information
I see that there are 10 probes that are tagged as "ignore", which
read.maimages ignores convenientl but, then, I can't visualize R and G
channels (or MA info when obtained) because of this inconsistency.
If I add, by hand, ten probes in the expression file, imageplot works
fine but this is not the right thing to do.
What is the convenient thing to do? Any suggestion?
Thank you in advance
Marc
--
-----------------------------------------------------
Marc Noguera i Julian, PhD
Genomics unit / Bioinformatics
Institut de Medicina Preventiva i Personalitzada
del C?ncer (IMPPC)
B-10 Office
Carretera de Can Ruti
Cam? de les Escoles s/n
08916 Badalona, Barcelona
Dear Marc,
There is a previous answer to another user with the same problem.
Source:
https://stat.ethz.ch/pipermail/bioconductor/2007-January/015532.html
I paste the text here (original by Dr. Gordon K Smyth)
---8<--------------
The error message is telling you that there aren't enough rows of data
for the size of the block.
The reason is that Agilent doesn't print rows for blank spots and the
like, so the block has
missing rows, and this causes a problem because the limma functions
assume complete blocks.
BTW, this is why the function read.maimages() didn't set the $printer
information automatically
for you. If the file had contained complete data for the block, then
it would have.
It is possible with a little R programming to expand out your data
vector stuff$Rb[,1] to be the
right length by adding NAs in the right places, so that you could use
imageplot(), but this bit of
code is not provided by limma or Bioconductor. Try this:
r <- stuff$genes$Row
c <- stuff$genes$Col
nr <- max(r)
nc <- max(c)
y <- rep(NA,nr*nc)
i <- (r-1)*nc+c
y[i] <- log2(stuff$Rb[,1])
imageplot(y,stuff$printer)
Best wishes
Gordon
--->8--------------
I hope that helps,
Best,
Juan Carlos Oliveros, Ph.D
CNB-CSIC, Madrid, Spain
Marc Noguera wrote:
> Hi all,
> I am trying to read and visualize data obtained from an agilent
chip.
>
> For this purpose I use limma package and the read.maimages function
as
> follows
>
> fileRG.raw <- read.maimages("File",source="agilent")
>
> FileRG gets read correctly. When I check the dimensions it shows to
have
> 243494 probes which seem to be correctly annotated. I, then attach
the
> layout for the chip from the GAL file:
>
> galinfo <- readGAL(fileGAL)
> fileRG.raw$printer<-getLayout(galinfo)
>
> and try to plot R/G according to this prnter layout:
>
> imageplot(log2(fileRG.raw$R),fileRG.raw$printer,zlim=c(0,9),main="R-
For.RAW")
>
> However, I obtain the following error:
>
>
>> Error in imageplot(log2(fileRG.raw$R), fileRG.raw$printer, zlim =
c(0, :
>> Number of image spots does not agree with layout dimensions
>>
> Which is due to the fact that the gal file has 912*267 dimension
> corresponding to 243504 probes. Checking the expression raw
information
> I see that there are 10 probes that are tagged as "ignore", which
> read.maimages ignores convenientl but, then, I can't visualize R and
G
> channels (or MA info when obtained) because of this inconsistency.
> If I add, by hand, ten probes in the expression file, imageplot
works
> fine but this is not the right thing to do.
>
> What is the convenient thing to do? Any suggestion?
>
> Thank you in advance
>
> Marc
>
>
