Hi,
another year goes by and aroma.affymetrix just turned six years old
and keeps growing. As we speak, a new version of aroma.affymetrix
v2.4.0 and friends is being rolled out on CRAN. As usual, it is
highly recommended to update. Update by running:
source("http://aroma-project.org/hbLite.R";
935595 ...
# Fit remaining units, i.e. SNPs (~5-10min/array)
units <- fit(plm, verbose=verbose)
str(units)
}
I get the following error:
20120112 16:45:44| Reading probe intensities from 56 arrays...done
Error in list(`#4: fit(plm, verbose = verbose)` = , `#4:
fit.ProbeLevelModel(plm
(~5-10s/array + some overhead)
> units <- fitCnProbes(plm, verbose=verbose)
> str(units)
> # int [1:945826] 935590 935591 935592 935593 935594 935595 ...
>
> # Fit remaining units, i.e. SNPs (~5-10min/array)
> units <- fit(plm, verbose=verbose)
> str(units)
>
Hi Henrik,
I have installed the latest aroma packages. Can you please advice how I can
setup aroma so that it knows where to look for the correct cytoband
information when drawing the cytoband in ChromosomeExplorer for displaying
copy number segmentation results?
I realized that in the old ar
Hi Henrik,
I have a set of SNP array data on the Illumina Omni1-Quad platform which we
use for inferring copy numbers. I can process these data using GenomeStudio
and export the LRR and BAF data. Previously I've created a custom chipType
in aroma for this array and loaded the LRR data into an
Yes,
the process is basically the same; replace AromaUnitTotalCnBinaryFile
with AromaUnitFracBCnBinaryFile. Put the TCN and the BAF data files
in the same directory. The BAF files should have the same name as the
TCN files but with an *,fracB.asb suffix. The use of
AromaUnitFracBCnBinaryFile is
Hi,
I didn't get around to fix that in aroma.* v2.4.0. The only thing I
can say now is to "hack" (read update) the GLAD package and update its
cytoband data. For instance, you can load that data by:
> pathname <- system.file("data/cytoband.RData", package="GLAD");
> keys <- load(pathname);
> ke
Sorry,
that should have been:
acs <- getAromaCellSequenceFile(cdf);
cells <- getAlleleCellPairs(cdf, verbose=verbose);
data <- getSnpNucleotides(acs, cells=cells, verbose=-50);
Look for the "Unique SNP positions:" output.
/Henrik
On Sun, Jan 8, 2012 at 3:23 PM, D Goode wrote:
> Hi Henrik,
>
>
Thanks, but I'm still having the same problem. Here's what happens:
> acs <- getAromaCellSequenceFile(cdf);
> cells <- getAlleleCellPairs(cdf, verbose=verbose);
Identifying the probe pairs...
Units:
NULL
Checking for cached results...
Found cached results
Checking for cached results...done
Hi.
The FIRMA scores are calculated as the *median* of the PLM residuals
(divided by an estimate of the std dev), cf. Eqn for F_ij (page 3) in
the Purdom et al. (2008) paper. Thus, in order to achieve F_ij =
-Inf, at least have of the PLM residuals (on the log scale) must be
-Inf. On the non-log
Ok, so it fails to identify any SNP positions based on your ACS file, cf.
> SNP positions:
> int [1:2410205] NA NA NA NA NA NA NA NA NA NA ...
> Tabulated SNP positions:
> character(0)
> Unique SNP positions:
> integer(0)
My guess is that your ACS file is incorrect (all zeros?). Did you
compare
Sorry Henrik, missed your post from last week. I downloaded your acs file.
It's the same size and the number of rows appear to be the same as the one
I made (as determined by aroma), but there appear to have differences in
file structure:
dgoode$ wc CytoScanHD_Array,HB20111008.acs
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