Hi.
On Tue, Feb 23, 2010 at 3:36 AM, Alfredo Hidalgo
<[email protected]> wrote:
> Hi!
>
> We are interested in running a GISTIC analysis on the data we obtained after
> segmentation with GLAD with Aroma, but there seems to be a problem regarding
> the start and end postions of the segments, which apparently do not match
> the physical positions of the markers file we are using for GISTIC.
I don't know what marker file you are using, but the locations for the
"markers" (units) used in the segmentation methods in aroma.affymetrix
is given by the UGP (unit genome position) file you are using. The
unit names are given by the CDF. You can find the UGP from the CDF as
follows:
cesN <- ...
glad <- GladModel(cesN);
cdf <- getCdf(cesN);
ugp <- getAromaUgpFile(cdf);
df <- data.frame(unitName=getUnitNames(cdf));
gp <- readDataFrame(ugp);
df <- cbind(df, gp);
>
> Does the segmentation reports the actual physical position of the first and
> last markers or does it reports other nearby position?
I returns whatever the glad() of the GLAD package returns. See
help("glad", package="GLAD") for more details.
If you wish to "troubleshoot" more at a low level, you can extract the
low-level data like this:
cn <- extractRawCopyNumbers(glad, array=1, chromosome=1);
data <- as.data.frame(cn);
pos <- data$x;
M <- data$cn;
and then use that to call glad(). That might help you.
>
> Another question, I have a copy number file obtained from paired analyisis
> in Partek Genomics Suite, and want to do the segmentation using GLAD or CBS.
> How can I incorporate my CN file into the Aroma pipeline to do the
> segmentation?
This requires that you first allocate so called binary CN files and
import the CN data to them. There is no pipeline to do this
automatically for Partek data, so you have to do it manually. This
requires a bit of understanding of the annotation data files involved
etc. It is explained in Vignette 'Creating binary data files
containing copy number estimates':
http://www.aroma-project.org/node/88
If you get that far, you can the, using the example in that vignette,
load the complete data set as:
ds <- AromaUnitTotalCnBinarySet$byName("MyDataSet,tagA,tagB",
chipType="HG-CGH-244A");
glad <- GladModel(ds);
and continue from there.
It is on the todo list to document all this better, but don't expect
anything soon.
/Henrik
>
> Thanks al lot!!
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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