CNAnorm Error -> dataFrame2object

Question

[karim]

Hey together,

I wanted to use CNAnorm for some analysis with my NGS-Data. And directly at the beginning I got an error, which I can´t solve by my self. (and with my self I mean Google)

So this is what I have done in R:

library(CNAnorm)
set.seed(31)
CN <- dataFrame2object("sample.tab")

(The sample.tab File I produced with bam2windows.pl)

I got this Error:

Error in dataFrame2object("sample.tab")
Data frame does not have column "Chr" Data frame does...."Pos"..."Test"..."Norm"

So I thought the sample.tab file isn´t correct, but it looks like this:

Chr Pos Test    Norm
KI270519.1  1   0   1
KI270519.1  15608   75  64
KI270519.1  31215   55  36
KI270519.1  46822   38  35
.........
........
.......
chr1....

So the file contains everything. Did anybody know where my fault is? Or know this problem?

Thanks! Karim

[Devon Ryan]

Are you reading in sample.tab first? I think that function needs a dataframe as input.

[karim]

THANK YOU!

It works!

sample <- read.table("sample.tab", header=TRUE)
CN <- dataFrame2object(sample)

[karim]

So, me again. Got another Problem with some of my Samples.

Sometimes I got this Error:

CN <- addDNACopy(CN)
Error in (function(...,row.names = NULL, check.rows = FALSE, check.names = TRUE,   :
arguments imply differing number of rows: 303, 301

after I done this:

library(CNAnorm)
set.seed(31)
sample <- read.table("sample.tab", header=TRUE)
CN <- dataFrame2object(sample)

CN <- addDNACopy(CN)

any ideas how I can solve that problem or why that error appears? Can I just delete 2 Rows?

Thanks for help!

[Devon Ryan]

I've never actually used this R package, so I can't help you with that one. You might have better luck posting on the bioconductor site, where hopefully the package maintainer will see it. For what it's worth, I'd guess that the problem is occurring at this line in the code, but one would need to play around with things to be sure.

[karim]

Thanks for your help!

I will post that problem on that site and if I will get an answer I will post it here.