

Dear All,

I am interested in analysing NimbleGen aCGH for copy number variation using R packages. I have tried few of the available packages but having problem with processing Nimblegen .pair files as most of the packages only accept log2 ratio of Cy3/5 as an input.  I managed to generate RGList object using RINGO package but got error messages when I tried to continue the analysis using snapCGH package. Please find below my session info:



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> setwd("/media/Data/Strains/test")
> 
> library(limma)
> library(DNAcopy)

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************

> library(snapCGH)


######################################################################################



Have fun with GLAD



For smoothing it is possible to use either

the AWS algorithm (Polzehl and Spokoiny, 2002)

or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008)



If you use the package with AWS, please cite:

Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)



If you use the package with HaarSeg, please cite:

Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)



For fast computation it is recommanded to use

the daglad function with smoothfunc=haarseg



######################################################################################



New options are available in daglad: see help for details.


> library(Ringo)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: RColorBrewer
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loading required package: grid
> 
> list.files(pattern="pair.txt")
[1] "27356202_532_pair.txt" "27356202_635_pair.txt"
> head(read.delim(file.path("27356202_532_pair.txt"),skip=1))[,c(1,4:7,9)]
      IMAGE_ID       PROBE_ID POSITION   X Y SEQ_URL
1 27356202_532 RANDOM00060001        0  25 1      NA
2 27356202_532 RANDOM00060002        0  27 1      NA
3 27356202_532 RANDOM00060003        0  29 1      NA
4 27356202_532 RANDOM00060004        0  43 1      NA
5 27356202_532 RANDOM00060005        0 297 1      NA
6 27356202_532 RANDOM00060006        0 371 1      NA
> read.delim(file.path("Targets.txt"), header=TRUE)
  SlideNumber           FileNameCy3           FileNameCy5  Cy3 Cy5
1           1 27356202_532_pair.txt 27356202_635_pair.txt test ref
> read.delim(file.path("SpotTypes.txt"), header=TRUE)
  SpotType GENE_EXPR_OPTION PROBE_ID Color
1    probe           BLOCK*        *  blue
2   RANDOM          RANDOM*        *   red
> RG1 <- readNimblegen("Targets.txt","SpotTypes.txt")
Reading targets file...
Reading raw intensities...
Read header information
Read /media/Data/Strains/test/27356202_532_pair.txt 
Read /media/Data/Strains/test/27356202_635_pair.txt 
Determining probe categories...
Matching patterns for: GENE_EXPR_OPTION PROBE_ID 
Found 2090470 probe 
Found 83156 RANDOM 
Setting attributes: values Color 
> head(RG1$R)
     27356202_635_pair
[1,]               268
[2,]               217
[3,]               182
[4,]               225
[5,]              7084
[6,]               207
> head(RG1$G)
     27356202_532_pair
[1,]               545
[2,]               645
[3,]               546
[4,]               589
[5,]              5974
[6,]               606
> 
> head(RG1$genes)
  GENE_EXPR_OPTION       PROBE_ID POSITION   X Y Status             ID
1           RANDOM RANDOM00060001        0  25 1 RANDOM RANDOM00060001
2           RANDOM RANDOM00060002        0  27 1 RANDOM RANDOM00060002
3           RANDOM RANDOM00060003        0  29 1 RANDOM RANDOM00060003
4           RANDOM RANDOM00060004        0  43 1 RANDOM RANDOM00060004
5           RANDOM RANDOM00060005        0 297 1 RANDOM RANDOM00060005
6           RANDOM RANDOM00060006        0 371 1 RANDOM RANDOM00060006
> 
> RG1$targets
  SlideNumber           FileNameCy3           FileNameCy5  Cy3 Cy5
1           1 27356202_532_pair.txt 27356202_635_pair.txt test ref
> RG1 <- readPositionalInfo(RG1, source = "nimblegen")
Error in data.frame(input$genes, Chr = as.numeric(chr), Start = (as.numeric(start)/1e+06),  : 
  arguments imply differing number of rows: 2173626, 0
> 
> RG1 <- read.clonesinfo("cloneinfo.txt", RG1)
Error in data.frame(RG$genes, Position, Chr = as.numeric(Chr)) : 
  arguments imply differing number of rows: 2173626, 0
> 
> RG1$printer <- getLayout(RG1$genes)
Error in getLayout(RG1$genes) : 
  gal needs to have columns Block, Row and Column

I would appreciate suggestion on how to resolve this problem. In addition, if anyone has a better way of analysing NimbleGen aCGH for copy number, I am open to suggestions.

Many thanks,

Adeolu

 		 	   		  
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