Thank you greatly for your help. A couple of additional questions:
1.) With the affxparser writeCdfx functions, it looks as though
you are directly writing the binary data of correct endianness rather
than inlining/swig-ing the fusion sdk functions. Am I understanding
this correctl
On 04/02/2009, at 1:24 PM, Sebastien Gerega wrote:
>
> Thanks Mark,
> that takes care of changing the colours but for some reason the names
> argument still isn't influencing anything. For example:
>
> bpstats = boxplotStats(getChipEffectSet(qam), type="NUSE")
> plotBoxplotStats(bpstats, boxfill
Thanks Mark,
that takes care of changing the colours but for some reason the names
argument still isn't influencing anything. For example:
bpstats = boxplotStats(getChipEffectSet(qam), type="NUSE")
plotBoxplotStats(bpstats, boxfill=c("red","blue","green"), names=c("G1",
"G2", "G3"))
does not c
Hi Sebastien.
My apologies, made a suggestion without running it myself. Try
something like:
qam <- QualityAssessmentModel(plm)
bpstats <- boxplotStats( getChipEffectSet(qam), type="RLE" )
# put in your specific arguments below ...
plotBoxplotStats(bpstats, boxwex=.2, boxfill=c("red","blue"
Hi Mark,
thanks for your reply. I had actually tried several commands along those
lines but always get the following:
Error in boxplot.stats(theta - medianLE, ...) :
unused argument(s) (boxwex = 0.4)
or:
Error in boxplot.stats(theta - medianLE, ...) :
unused argument(s) (boxfill = "blue")
T
Hi Sebastien.
Note that plotRle() eventually makes a call to 'bxp' (in the graphics
package that is loaded by default) and any/all arguments are passed on.
Have a look at ?bxp for what you can specify.
For example:
[...]
qamTr <- QualityAssessmentModel(plmTr)
plotRle(qamTr, boxwex=[something]
Hi,
is there a way to change the colour of each individual bargraph when calling
plotRle? I would like to make the colours correspond to test groups.
thanks,
Sebastien
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the late
Hi,
there are no methods of such analysis available in aroma.affymetrix,
and there is no time line for implementing that. It is of course on
our wishlist, though. Note also that "LOH analysis" is rather
unspecific; there are many different ways to infer LOH, of which some
depend on what kind of
Hi,
especially those zoom levels generate very large PNGs. They might be
too large for your PNG device driver. Depending on your system, there
are few different PNG drivers available to R. You can override the
one that aroma.affymetrix uses, but overriding the findPngDevice()
function.
Search
Some comments:
1. The problem occurs in the internal method getUnitGroupCellMap().
This is only called once per chip type, regardless if you restart R or
not. The result is memoized (=cached to file) and reused in the
future. Thus, if you can get it to work once, you won't have the
problem anym
Sorry, changed network points and reposted by accident. Thanks for
your help. This should be enough to get me thinking for a bit.
On Feb 3, 2009, at 3:23 PM, Henrik Bengtsson wrote:
>
> Ok, sorry I didn't answer you question explicitly. No, they do not
> have to contain ChrX and ChrY data.
Ok, sorry I didn't answer you question explicitly. No, they do not
have to contain ChrX and ChrY data. However, but independent of your
question, I would recommend that you import all annotation data
available, since that might become of interest in future usage.
Currently part of the code is h
Hi,
the factor of two has to do with the number of parameters
estimated/stored, i.e. storing theta, vs (thetaA, thetaB). I cannot
reproduce this, but I one guess is that you have tried both
combineAlleles=TRUE and combineAlleles=FALSE and somehow there exist
cached indices that are reused from o
Do they ufl/ugp/acc files need to be build with X and Y chromosomes
included? If so, this won't be too hard to fix.
On Jan 30, 9:50 pm, David Rosenberg
wrote:
> As I think about this further, it occurs to me that there are other
> potential problems with this chip/cdf. I was looking at the
Hi,
I'm swamped and still haven't had a chance to create a real fix, but a
quick fix is to override the arguments that defaults to "-XY", but
replacing them with an integer/index vector specifying the *units* on
the autosomal chromosomes, that is, the ones that are are expected to
be copy neutral
Hi Michal,
it shouldn't be tedious at all - did you follow the instructions?
source("http://www.braju.com/R/hbLite.R";)
hbInstall("aroma.affymetrix")
URL: http://groups.google.com/group/aroma-affymetrix/web/download-install
That should install R.huge v0.1.6 as well, but if it for some reason
d
Hello,
I am trying to install aroma.affymetrix on R 2.8.1 (and the
Bioconductor version that goes with it).
After a long and tedious process of downloading missing packages, I'm
stuck at the following:
Error: package 'R.huge' 0.1.5 was found, but >= 0.1.6 is required by
'aroma.affymetrix'
Is i
Do they ufl/ugp/acc files need to be build with X and Y chromosomes
included? If so, this won't be too hard to fix.
On Jan 30, 9:50 pm, David Rosenberg
wrote:
> As I think about this further, it occurs to me that there are other
> potential problems with this chip/cdf. I was looking at the
Dear all,
AFAIK there is no method for LOH / UPD analysis implemented in a.a
(yet?)? Is there a timeline for that? Does anybody have an established
workflow for that, e.g. low level processing in a.a, and then using a
separate solution?
Any comments are appreciated!
Thanks,
Michael.
IMB, Univ
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