Hi,
I am new using pdInfoBuilder, so I may be missing something. I am trying to
use pdInfoBuilder to make an annotation package. However, I get an error
after the makePdInfoPackage(seed, destDir = "./") command.

Error in aggregate.data.frame(as.data.frame(x), ...) :
  no rows to aggregate

 Has anybody encountered this message?

Thanks!,

Alex

Here is my list of commands:

> library(pdInfoBuilder)
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: RSQLite
Loading required package: DBI
Loading required package: affxparser
Loading required package: oligo
Loading required package: oligoClasses
Loading required package: preprocessCore
Welcome to oligo version 1.10.2
> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863"
> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE))
[1] 
"/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDIP_HX1.
ndf"
> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1])
[1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys"
> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE))
[1] 
"/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDIP_HX1.
pos"
> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile =
pos, author = "AR", biocViews
= "AnnotationData", genomebuild = "HG 18", organism = "Human", species =
"Homo Sapiens")
> makePdInfoPackage(seed, destDir = "./")
============================================================================
====
Building annotation package for Nimblegen Tiling Array
NDF:  081229_HG18_Promoter_MeDIP_HX1.ndf
POS:  081229_HG18_Promoter_MeDIP_HX1.pos
XYS:  38693602_532.xys
============================================================================
====
Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK
Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK
Merging NDF and POS files... OK
Parsing file: 38693602_532.xys ... OK
Error in aggregate.data.frame(as.data.frame(x), ...) :
  no rows to aggregate
Calls: makePdInfoPackage ... aggregate -> aggregate.default ->
aggregate.data.frame
In addition: Warning message:
In is.na(ndfdata[["SIGNAL"]]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Execution halted



This email is intended only for the use of the individua...{{dropped:6}}

