On Wed, Apr 16, 2014 at 5:44 AM, Juan José Lozano Salvatella
<juanjo.loz...@ciberehd.org> wrote:
> Hi Henrik
>
> Thanks!! I understand. It seems X-files. I dont known what happens because i
> use the same script. May be the problem is related to past reruns in other
> computer (and probably other versions).
I'm sure there are no aliens or higher powers involved; instead
there's probably a very simple answer to this.
>
> When i use the script in a new rawdata folder (moving the cels and thus no
> using probedata and other temporary directories)
> the results are the expected.
The way I read this is that you are forcing a new AS-CRMAv2 run.
Since AS-CRMAv2 is completely deterministic, I don't see how this
makes a difference. I still also don't understand if you are saying
whether this solved your problem? Can you still reproduce the
original problem or is appearing "randomly"?
Looking at your two (Chr20) plots that you've sent,
'double_problem_cnv.png' and 'file_corrected.png' it doesn't look like
to raw data is the same. So, to simplify your life, you could start
by asserting that you get the exact same 'data' object when you rerun
AS-CRMAv2. If that is not the case, the problem is unrelated to PSCBS
and that should be troubleshooted first.
I would save 'data' after these steps:
data <- extractPSCNArray(res$total);
dimnames(data)[[3]] <- names(pair);
saveObject(data, "data-run1.Rbin")
then re-run in a different directory and save as:
saveObject(data, "data-run2.Rbin")
then you can compare the two outputs:
library("R.utils")
data1 <- loadObject("data-run1.Rbin")
data2 <- loadObject("data-run2.Rbin")
stopifnot(all.equal(data1, data2))
As a I said above, I would be surprised if you don't get that 'data1'
and 'data2' are equal/identical.
/Henrik
>
> Yes, i will check the pscbs vignette.
>
> Best
>
> Juanjo
>
>
> El martes, 15 de abril de 2014 18:43:42 UTC+2, Henrik Bengtsson escribió:
>>
>> Hi,
>>
>> from the script you attached I see that you're looking at the online
>> vignette
>>
>> http://aroma-project.org/vignettes/PairedPSCBS-lowlevel
>>
>> FYI, there is also a vignette in the PSCBS package [e.g.
>> cran.r-project.org/web/packages/PSCBS] that you might find useful,
>> particularly on how to avoid segment centromeres.
>>
>> On Tue, Apr 15, 2014 at 4:32 AM, Juan José Lozano Salvatella
>> <juanjo...@ciberehd.org> wrote:
>> > Hi Henrik
>> >
>> >
>> > when i run the two samples in a same directory ( a new (re) run without
>> > others pairs) . The results are ok.
>>
>> This is not clear to me; are you saying that the script you attached
>> solved the problem, but what you did before (not shown) does not work?
>> If so, what did you do before?
>>
>> /Henrik
>>
>> >
>> >
>> > my details:
>> >
>> > sessionInfo()
>> > R version 3.0.1 (2013-05-16)
>> > Platform: x86_64-pc-linux-gnu (64-bit)
>> >
>> > locale:
>> > [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C
>> > [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8
>> > [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
>> > [7] LC_PAPER=C LC_NAME=C
>> > [9] LC_ADDRESS=C LC_TELEPHONE=C
>> > [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
>> >
>> > attached base packages:
>> > [1] stats graphics grDevices utils datasets methods base
>> >
>> > other attached packages:
>> > [1] sfit_0.3.0 aroma.light_1.30.5 matrixStats_0.8.14
>> > [4] aroma.affymetrix_2.12.0 aroma.core_2.12.1 R.devices_2.8.2
>> > [7] R.filesets_2.4.0 R.utils_1.29.8 R.oo_1.18.0
>> > [10] affxparser_1.32.3 R.methodsS3_1.6.1
>> >
>> > loaded via a namespace (and not attached):
>> > [1] aroma.apd_0.5.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.34.0
>> > [5] PSCBS_0.40.4 R.cache_0.9.0 R.huge_0.8.0 R.rsp_0.15.0
>> > [9] splines_3.0.1 tools_3.0.1
>> >
>> > Any comments are wellcome!
>> >
>> > Thanks a lot
>> >
>> > Best
>> >
>> > Juanjo
>> >
>> >
>> >
>> >
>> > El lunes, 14 de abril de 2014 23:51:20 UTC+2, Henrik Bengtsson escribió:
>> >>
>> >> Hi,
>> >>
>> >> agree, that certainly doesn't look correct - but there's probably a
>> >> simple explanation/fix. Before anything else, what version of PSCBS
>> >> are you running, i.e. what's your sessionInfo(). Also, exactly what
>> >> does you script look like, and if you have a problematic sample you
>> >> could share with me, that would help me reproduce this and help you.
>> >>
>> >> Cheers,
>> >>
>> >> Henrik
>> >>
>> >> On Mon, Apr 14, 2014 at 4:55 AM, Juan José Lozano Salvatella
>> >> <juanjo...@ciberehd.org> wrote:
>> >> > Hi
>> >> >
>> >> > I run the Vignette: Paired parent-specific copy-number segmentation
>> >> > (Paired
>> >> > PSCBS) and we obtain some segments as the attached file.
>> >> >
>> >> > CNV segments are diffcult to explain. Could you explain this?
>> >> >
>> >> > Thanks a lot in advance
>> >> >
>> >> > Best
>> >> >
>> >> > Juanjo
>> >> >
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