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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