[R] unable to compute MAD in aCGH package

From: <Sze_Sing_LEE/DMO/NCC_at_nccs.com.sg>
Date: Mon 03 Oct 2005 - 16:13:04 EST


Hi,

I am currently using the aCGH package in R version 2.1.0 Windows with some supporting packages (eg. cluster) built under R 2.1.1.Using aCGH package, I am able to identify regions of genomic aberrations in my cell lines using the HMM model. However, when I tried to use aCGH for my paraffin embeded tumour sample, I got the following warning.

Warning: MAD could not ben computed for one of the samples.

I had used the same R commands for both my tumour samples and cell lines. I had performed HMM partioning using the model AIC with a merging step afterwards with the threshold set at 0.25.

Therefore, I have a few questions:

  1. Could it be that my sample are 'noisy' for aCGH to compute? DNA extracted from paraffin embeded tissue is of a poorer quality compared to cell line DNA. Is there a limitation to the data distribution itself?
  2. Or could I change the default parameters in aCGH in order to analyse my data?
  3. A more general question, could we combine packages built under different versions? As mentioned above, I am using version 2.1.0 but some of my packages involved in aCGH are built under version 2.1.1.

Thank you.

Sincerely,
Louise

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