I have to normalize my one color samples (gpr) before use SAM or PAM.
  I have 8 samples (4 normal against 4 Treated), so after normalization (between samples) i'd like to use two class unpaired script by SAM.
  So the problem is the preprocessing (background subtract, filter on flags or percentual of data missings, normalization) of my one color data.
  Few people use one color gpr so this analysis could be a problem for me.
  Thank you
   
  

"Paquet, Agnes" <apaquet@medsfgh.ucsf.edu> ha scritto: 
        v\:* {behavior:url(#default#VML);}  o\:* {behavior:url(#default#VML);}  w\:* {behavior:url(#default#VML);}  .shape {behavior:url(#default#VML);}                Hi,
   
  Most diagnostic plots in arrayQuality will be generated for two-color array only, which explains why you are getting an error message when you call maQualityPlots. You can use the function PRv9mers() in arrayQuality to take a look at some one-color exploratory plots, but keep in mind that this function is designed to check print quality, not hybridization quality…
   
  The same applies to many normalization methods used for two-color spotted arrays, like print-tip loess which is the default in marray. These methods are based on log ratios and log-intensity and most functions will not calculate them for one color arrays.
   
  I have never done any analysis on one color spotted array, so I don’t think I can advice you on this topic. Could you please give more details on the experiment you are working on and the type of analysis you are thinking about? That way, maybe somebody else from the list could help you get started.
   
  Regards,
   
  Agnes
   
   
   
      
---------------------------------
  

Sent: Thursday, December 01, 2005 9:05 AM
To: Paquet, Agnes
Cc: bioconductor@stat.math.ethz.ch
Subject: RE: [BioC] gpr one color

   
    Thanks.
Now i can open my one color gpr.
When the preprocessing is completed (array quality and normalization), i'd like export my normalized data  to a text files to analyze with SAM and PAM( or samr,pamr), but i cant' t do it (see below):

     

    > sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32 
attached base packages:
[1] "grid"      "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"  "base"     
other attached packages:
      mclust arrayQuality     gridBase       hexbin   colorspace      convert      Biobase       marray        limma 
    "2.1-11"      "1.4.0"      "0.4-1"      "1.4.0"        "0.9"      "1.4.0"      "1.8.0"      "1.8.0"      "2.4.4" 
       beta7 
     "0.5.5" 
> TargetInfo<-read.marrayInfo("Target.txt")
> TargetInfo
An object of class "marrayInfo"
@maLabels
[1] "43.gpr" "44.gpr" "45.gpr"
@maInfo
  FileNames SubjectID  Cy5 Date of Bl Draw Date of Scan
1    43.gpr         1 b9 +         2004.10.11   2005.07.25
2    44.gpr         2 b9 -         2004.01.16   2005.08.07
3    45.gpr         3 b9 -         2004.01.16   2005.08.07
@maNotes
[1] "Target.txt"

    > mraw<- read.GenePix(name.Rf=NULL, name.Rb=NULL,name.Gf="F635 Median", name.Gb="B635 Median",DEBUG=TRUE)
[1] "43.gpr" "44.gpr" "45.gpr"
[1] "Reading Galfile ... "
[1] "done \n "
character(0)
Setting up controls status ... Generate controls 
probes 
 11520 
done 
 Calling read.marrayRaw ... 
Reading ...  43.gpr 
Reading ...  44.gpr 
Reading ...  45.gpr 
> maQualityPlots(mraw)
Error: subscript out of bounds
In addition: Warning message:
is.na() applied to non-(list or vector) in: is.na(rows) 
> normdata<-maNorm(mraw)
Error: subscript out of bounds
In addition: Warning message:
is.na() applied to non-(list or vector) in: is.na(rows) 
> write.marray(mraw)
Error in data.frame(..., check.names = FALSE) : 
        arguments imply differing number of rows: 11520, 0

     

    
Can you help me?
Thank you

     

    *******************************************************************************************

    
"Paquet, Agnes" <apaquet@medsfgh.ucsf.edu> ha scritto: 

      Hi,

     

    I think the problem comes from the underlying implementation of marray. Basically, read.GenePix is creating an object to store the data using the number of columns in the green channel (name.Gf). Since you don’t have any, the code is doing something funny. One way around it is to read your data in the green channel instead of the red (just remember that your array is red, not green) and it seems to work fine with my configuration. I used the following code:

     

    > test <- read.GenePix(name.Rf=NULL, name.Rb=NULL,name.Gf="F635 Median", name.Gb="B635 Median",DEBUG=TRUE)

    [1] "1NT.gpr"

    [1] "Reading Galfile ... "

    [1] "done \n "

    character(0)

    Setting up controls status ... Generate controls 

     

    probes 

     11520 

    done 

     Calling read.marrayRaw ... 

    Reading ...  1NT.gpr 

    > 

     

    My computer configuration is:

    > sessionInfo()

    R version 2.2.0, 2005-10-06, i386-pc-mingw32 

     

    attached base packages:

    [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"  "base"     

     

    other attached packages:

     marray   limma 

    "1.8.0" "2.2.0" 

    > 

     

    I hope that will help.

     

    Best,

     

    Agnes

     

    
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