Hi all,

 

I ran the default example for the aCGH package up to and including the
LOWESS function without any problems.  I then used a GEO dataset GSE2631 and
platform GPL2024 (processed to fit aCGH's conventional rows/columns rules).
The rows and IDs are the same in both inputs.  This is what I ran,

 

library(aCGH)

datadir <- system.file(package = "aCGH")

datadir_data <- paste(datadir, "/dataset", sep="")

datadir_operating <- paste(datadir, "/Operating.Files", sep="")

 

# reads in array data & annotations

log2.ratios <- read.table(file = file.path(datadir_data,
"log2.ratios..txt"), header = T, sep = "\t", quote = "", comment.char = "")

clones.info <- read.table(file = file.path(datadir_operating,
"clones.info..txt"), header = T, sep = "\t", quote = "", comment.char = "")

#pheno.type <- read.table(file = file.path(datadir, "pheno.type.ex.txt"),
header = T, sep = "\t", quote = "", comment.char = "")

 

# creates aCGH object and processes data

ex.acgh <- create.aCGH(log2.ratios, clones.info)

ex.acgh <- aCGH.process(ex.acgh, chrom.remove.threshold = 23, prop.missing =
0.25, sample.quality.threshold = 0.4, unmapScreen = TRUE, dupRemove = FALSE)

 

 

The output was:

 

DMPC-HFF#1-61H8          1651 1652 

Error in max(..., na.rm = na.rm) : invalid 'type' (character) of argument

In addition: There were 50 or more warnings (use warnings() to see the first
50)

> warnings()

1: argument is not numeric or logical: returning NA in: mean.default(newX[,
i], ...) 

2: argument is not numeric or logical: returning NA in: mean.default(newX[,
i], ...)

...

 

It seems like it can't differentiate the chromosome numbers but I'm not sure
how to fix this.  The sample clones.info file were missing some of the clone
positions that were in my platform, but my platform turns out to have only
1957 clones (vs. the sample one which had more than 2000).  Any help?

 

Thanks in advance,

 

Jason


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