[BioC] snapCGH package - processCGH

[Henrique Proença]

Hello,

I am doing some analysis of Agilent CGH and I found out that if I have 
some data without duplicates the function processCGH crashes.

> Error in processCGH(MA, method.of.averaging = methodOfAveraging, ID = meanIDcol,  : 
>   object "segList" not found
> In addition: Warning message:
> In getChrInfo(MA) : NAs introduced by coercion


Analyzing the function processCGH, I found out that the error could be 
related with a miss location of a "}"
I mean, instead of being after the following code

  dupl <- duplicated(MA$genes$ID)
  segList <- list()
  segList$M.observed <- MA$M[!dupl, , drop = FALSE]
  segList$genes <- MA$genes[!dupl, ]
  }

The if (any(tbl > 1))  should be closed before:

  }
  dupl <- duplicated(MA$genes$ID)
  segList <- list()
  segList$M.observed <- MA$M[!dupl, , drop = FALSE]
  segList$genes <- MA$genes[!dupl, ]


If I change the code, it seems to work, could you please tell me if this 
is a bug?



My System information is:
R version 2.7.0 (2008-04-22)
i386-pc-mingw32


attached base packages:
  [1] splines   grid      tools     stats     graphics  grDevices utils 
     datasets  methods   base

other attached packages:
  [1] snapCGH_1.8.0        RUnit_0.4.17         aCGH_1.14.0 
sma_0.5.15           multtest_1.20.0
  [6] cluster_1.11.10      GLAD_1.16.0          DNAcopy_1.14.0 
tilingArray_1.18.0   pixmap_0.4-7
[11] geneplotter_1.18.0   annotate_1.18.0      xtable_1.5-2 
AnnotationDbi_1.2.0  RSQLite_0.6-8
[16] DBI_0.2-4            genefilter_1.20.0    survival_2.34-1 
vsn_3.6.0            limma_2.14.0
[21] lattice_0.17-6       strucchange_1.3-3    sandwich_2.1-0 
zoo_1.5-3            RColorBrewer_1.0-2
[26] affy_1.18.0          preprocessCore_1.2.0 affyio_1.8.0 
Biobase_2.0.0

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-22


Thanks in advance.

Sorry to send you this email, but I didn't find the email of the snapCGH 
package maintainer.

-- 
Regards
Henrique Proença