Re: [aroma.affymetrix] Doubts in PSCBS segments
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 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 > > -- > -- > 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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Doubts in PSCBS segments
Hi Henrik when i run the two samples in a same directory ( a new (re) run without others pairs) . The results are ok. 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-8LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=es_ES.UTF-8LC_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_2.4.0R.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_0.6.4DNAcopy_1.34.0 [5] PSCBS_0.40.4R.cache_0.9.0 R.huge_0.8.0R.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 > > 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 > > > > -- > > -- > > 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. > > > > > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to > > aroma-af...@googlegroups.com > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to aroma-affymetr...@googlegroups.com . > > For more options, visit https://groups.google.com/d/optout. > -- -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. <> rLOH_CRC37.r Description: Binary data
Re: [aroma.affymetrix] Doubts in PSCBS segments
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 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-8LC_COLLATE=es_ES.UTF-8 > [5] LC_MONETARY=es_ES.UTF-8LC_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_2.4.0R.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_0.6.4DNAcopy_1.34.0 > [5] PSCBS_0.40.4R.cache_0.9.0 R.huge_0.8.0R.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 >> 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 >> > >> > -- >> > -- >> > 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. >> > >> > >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group with website http://www.aroma-project.org/. >> > To post to this group, send email to aroma-af...@googlegroups.com >> > To unsubscribe and other options, go to >> > http://www.aroma-project.org/forum/ >> > >> > --- >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to aroma-affymetr...@googlegroups.com. >> > For more options, visit https://groups.google.com/d/optout. > > -- > -- > 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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubsc
Re: [aroma.affymetrix] Doubts in PSCBS segments
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). 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. 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 > > 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-8LC_COLLATE=es_ES.UTF-8 > > [5] LC_MONETARY=es_ES.UTF-8LC_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_2.4.0R.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_0.6.4DNAcopy_1.34.0 > > [5] PSCBS_0.40.4R.cache_0.9.0 R.huge_0.8.0R.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 > >> 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 > >> > > >> > -- > >> > -- > >> > 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. > >> > > >> > > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "aroma.affymetrix" group with website http://www.aroma-project.org/. > >> > To post to this group, send email to aroma-af...@googlegroups.com > >> > To unsubscribe and other options, go to > >> > http://www.aroma-project.org/forum/ > >> > > >> > --- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "aroma.affymetrix" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send > >> > an > >> > email to aroma-affymetr...@googlegroups.com. > >> > For more options, visit https://groups.google.com/d/optout. > > > > -- > > -- > > 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. > > > > > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to > > aroma-af...@googlegroups.com > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > --- > > You received this mess
Re: [aroma.affymetrix] Doubts in PSCBS segments
On Wed, Apr 16, 2014 at 5:44 AM, Juan José Lozano Salvatella
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
>> 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-8LC_COLLATE=es_ES.UTF-8
>> > [5] LC_MONETARY=es_ES.UTF-8LC_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_2.4.0R.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_0.6.4DNAcopy_1.34.0
>> > [5] PSCBS_0.40.4R.cache_0.9.0 R.huge_0.8.0R.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
>> >> 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
>> >> >
>> >> > --
>> >> > --
>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> > latest
>> >> > version of the package,
Re: [aroma.affymetrix] Doubts in PSCBS segments
Hi again.
Yes, it's odd to the eye that PSCBS fail to segment this sample; it
looks as it should pick it up at either the TCN or the following DH
segmentation step. My guess is that it fails to detect the change
point it in the TCN step is that there are enough outliers to mess up
the underlying assumption of a well behaving Gaussian distribution.
If you drop TCN outliers before calling the segmentation method, it
does work as expected, e.g.
data <- read.table("chr20_fail.csv", sep="\t", dec=",", header=TRUE)
data <- dropSegmentationOutliers(data)
fit <- segmentByPairedPSCBS(data)
Dropping TCN outliers is discussed in the 'Parent-specific copy-number
segmentation using Paired PSCBS' vignette part of the package
[http://cran.r-project.org/web/packages/PSCBS]. There we write that
the step is optional, but maybe should also write that we recommend it
(we use it all the time ourselves). BTW, in the same document, we
also show how to avoid segmenting over centromeres, e.g.
data <- read.table("chr20_fail.csv", sep="\t", dec=",", header=TRUE)
data <- dropSegmentationOutliers(data)
gaps <- findLargeGaps(data, minLength=1e+06)
knownSegments <- gapsToSegments(gaps)
fit <- segmentByPairedPSCBS(data, knownSegments=knownSegments)
Hope this helps
Henrik
On Thu, Apr 17, 2014 at 3:20 AM, Juan José Lozano Salvatella
wrote:
> Hi Henrik
>
> Thanks for your help!!
>
> Yes, the data.frame before PSCBS are different. Attached chr20 files from
> the good and bad results.
>
> Anyway, when you plot both results you can reproduce the plots...
>
> the only difference is the dataSet <- "RM";
>
> diff rLOH_CRC37_fail.r rLOH_CRC37.r
>
> 6c6
> < dataSet <- "RM";
> ---
>> dataSet <- "lite";
>
> In any case i think PSCBS must to segment better the "fail" version...at
> least at the cnv level
>
> Best
>
> Juanjo
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> El jueves, 17 de abril de 2014 02:22:58 UTC+2, Henrik Bengtsson escribió:
>>
>> On Wed, Apr 16, 2014 at 5:44 AM, Juan José Lozano Salvatella
>> 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
>> >> 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)
