[BioC] snapCGH and Nimblegen arrays

[Gareth Wilson]

Dear All,

I'm interested in identifying CNV regions using two Nimblegen arrays -
both of which are input vs input arrays.

A suitable package, I think, is snapCGH. I'm pretty new to both R and
array analysis, however, I came across a post in the BioC mailing list,
which included two R scripts (processNimblegenData.R and
NimblegenUtilityFunctions.R), that utilised snapCGH and which seemed to
do what I was after.

I worked my way through the commands in processNimblegenData.R.
Unfortunately I got the following error when I tried to run the
processCGH method:

Error in `row.names<-.data.frame`(`*tmp*`, value = c(1L, 0L)) :
  invalid 'row.names' length

I had previously received warnings after a couple of other commands:

NimblegenHeatmaps(RG)

Processing heat maps...
G:ChipNo =  1 (ChipID =  8898202_532.pair )  Error in image.default(x =
(-1:770), y = (-1:1026), z = zmat, col = col,  :
  dimensions of z are not length(x)(-1) times length(y)(-1)

RG <- readPositionalInfo(RG, source = "nimblegen")

Warning message:
In data.frame(input$genes, Chr = as.numeric(chr), Start =
(as.numeric(start)/1e+06),  :
  NAs introduced by coercion



If it helps, my MAlist object looks like this:

An object of class "MAList"
$genes
       IMAGE_ID GENE_EXPR_OPTION                  SEQ_ID
PROBE_ID
829 8898202_532           BLOCK1 chr11:60023467-60024667
CHR11FS060023489
830 8898202_532           BLOCK1 chr11:60023467-60024667
CHR11FS060023569
831 8898202_532           BLOCK1 chr11:60023467-60024667
CHR11FS060023674
832 8898202_532           BLOCK1 chr11:60023467-60024667
CHR11FS060023764
833 8898202_532           BLOCK1 chr11:60023467-60024667
CHR11FS060023839
    Position   X   Y MATCH_INDEX SEQ_URL Chr    Start      End
829 60.02349 253 327    71842416      NA  NA 60.02349 60.02349
830 60.02357  48  92    71842417      NA  NA 60.02357 60.02357
831 60.02367  61  95    71842418      NA  NA 60.02367 60.02367
832 60.02376 299  87    71842419      NA  NA 60.02376 60.02376
833 60.02384 215 433    71842420      NA  NA 60.02384 60.02384
71204 more rows ...

$design
[1] -1 -1

$M
     8898202_532.pair 8898302_532.pair
[1,]        0.4152331       0.19290427
[2,]        0.1847667       0.39225230
[3,]        0.1450361       0.01751499
[4,]        0.2403561      -0.06698188
[5,]        0.2845034       0.12658724
71204 more rows ...

$A
     8898202_532.pair 8898302_532.pair
[1,]         10.58601         10.43860
[2,]         10.44993         10.32034
[3,]         10.41355         10.09611
[4,]         10.48482         10.13966
[5,]         10.63333         10.50491
71204 more rows ...



I was wondering whether anyone had any idea as to how I could overcome
these issues. Any help would be appreciated.

Many Thanks

Gareth.

-----
Dr Gareth A Wilson

Medical Genomics Group

UCL Cancer Institute
Paul O'Gorman Building
University College London
72 Huntley Street
London
WC1E 6BT

tel: +44 (0) 20 7679 0999
-----


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