Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Dear Henrik,
thank you so much for your complete answer! I'll try your suggestions on
monday and give you some feedback!
Best,
Xavi.
2011/6/17 Henrik Bengtsson
> Hi.
>
> On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole wrote:
> > Hi all,
> > I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I
> > have tumor and normal samples, and now I want to apply an unpaired CBS
> > model. I know ho to do the paired model, but I'm not sure is this code is
> > right for the unpaired one:
> > library(aroma.affymetrix);
> > library(aroma.cn);
>
> No need for 'aroma.cn' here.
>
> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
> > options(digits=4);
> > setOption(aromaSettings, "memory/ram", 500.0)
> > # Verify that the data set can be located:
> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> > dataSet <- "CEL_files";
>
> Each analysis you run should have a unique data set name, i.e. what
> name should you use next time? I recommend to use a much more
> informative name of your data set - something that reflects the
> project name and/or the investigator and the year, or similar.
>
> > dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
> > setFullName(dsR, dataSet);
>
> No need to do this.
>
> > # Using CRMAv2
> > dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE,
> verbose=verbose);
>
> Since you've already have setup an AffymetrixCelSet object ('dsR')
> above, you should use that instead:
>
> dsList <- doCRMAv2(dsR, combineAlleles=FALSE, verbose=verbose);
>
> or even shorter for allele-specific analysis, you can equivalently do:
>
> dsList <- doASCRMAv2(dsR, verbose=verbose);
>
> > dsC <- dsList$total;
> > # Splitting the dataset in normal-tumor pairs
> > infoSamples <- read.table("samples.txt", sep="\t", header=TRUE, as.is
> =TRUE,
> > strip.white=TRUE);
> > #Rows in this file are in the same order as arrays in the aroma dataset.
> > idxN <- which(infoSamples$type=="Normal");
> > idxT <- which(infoSamples$type=="Tumor");
>
> This is a bit dangerous since it assumes that the rows in your
> 'samples.txt' file is ordered the same way as the files on this. At
> least I would assert that that is the case by something like:
>
> stopifnot(all(infoSamples$name == getName(dsC));
>
> or similar.
>
> > dsN <- extract(dsC, idxN);
> > dsT <- extract(dsC, idxT);
> > # Circular binary segmentation T vs N: Paired model (first N sample pairs
> > with first T sample)
> > cns <- CbsModel(dsT, dsN);
> > fit(cns, verbose=TRUE);
> > regDatList <- getRegions(cns);
>
> Yes, this does a tumor-normal paired CBS segmentation (and extracts
> the table of regions afterward).
>
> > # Circular binary segmentation T vs N: Unpaired: I DON'T KNOW IF THIS IS
> > CORRECT (cns.unpaired keeps me telling that the reference sample is made
> of
> > 102 files instead of one!).
> > avgN <- getAverageFile(dsN);
>
> This is the correct command and 'avgN' should *indeed* a single file
> ("array") here. You should be able verify by looking at what:
>
> print(avgN);
>
> returns.
>
> > cns.unpaired <- CbsModel(dsT, avgN);
>
> This should work, because 'dsT' is a data set; verify by
>
> print(dsT);
>
> If it doesn't work please let us know what:
>
> print(dsT);
> print(avgN);
>
> returns and what the complete error message is.
>
> > fit(cns.unpaired, verbose=TRUE);
> > regDatList.unpaired <- getRegions(cns.unpaired);
>
> [snip]
>
> I'll answer your second question in a separate thread ...and when I
> find the time.
>
> /Henrik
>
> > Thank you very much for your help!
> > Best,
> > Xavi.
> > #SESSION INFO
> >> sessionInfo()
> > R version 2.13.0 (2011-04-13)
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> > locale:
> > [1] C
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> > other attached packages:
> > [1] DNAcopy_1.26.0 aroma.cn_0.5.2 aroma.affymetrix_2.1.0
> > [4] aroma.apd_0.1.8affxparser_1.24.0 R.huge_0.2.2
> > [7] aroma.core_2.1.0 aroma.light_1.20.0 matrixStats_0.2.2
> > [10] R.rsp_0.5.3R.cache_0.4.2 R.filesets_1.0.1
> > [13] digest_0.5.0 R.utils_1.7.5 R.oo_1.8.0
> > [16] R.methodsS3_1.2.1
> > loaded via a namespace (and not attached):
> > [1] tools_2.13.0
> >
> > --
> > 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/
> >
>
> --
> 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(), a
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
On Fri, Jun 17, 2011 at 12:15 PM, Henrik Bengtsson
wrote:
> Hi.
>
> On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole wrote:
>> Hi all,
>> I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I
>> have tumor and normal samples, and now I want to apply an unpaired CBS
>> model. I know ho to do the paired model, but I'm not sure is this code is
>> right for the unpaired one:
>> library(aroma.affymetrix);
>> library(aroma.cn);
>
> No need for 'aroma.cn' here.
>
>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
>> options(digits=4);
>> setOption(aromaSettings, "memory/ram", 500.0)
>> # Verify that the data set can be located:
>> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
>> dataSet <- "CEL_files";
>
> Each analysis you run should have a unique data set name, i.e. what
> name should you use next time? I recommend to use a much more
> informative name of your data set - something that reflects the
> project name and/or the investigator and the year, or similar.
>
>> dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
>> setFullName(dsR, dataSet);
>
> No need to do this.
>
>> # Using CRMAv2
>> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
>
> Since you've already have setup an AffymetrixCelSet object ('dsR')
> above, you should use that instead:
>
> dsList <- doCRMAv2(dsR, combineAlleles=FALSE, verbose=verbose);
>
> or even shorter for allele-specific analysis, you can equivalently do:
>
> dsList <- doASCRMAv2(dsR, verbose=verbose);
>
>> dsC <- dsList$total;
>> # Splitting the dataset in normal-tumor pairs
>> infoSamples <- read.table("samples.txt", sep="\t", header=TRUE, as.is=TRUE,
>> strip.white=TRUE);
>> #Rows in this file are in the same order as arrays in the aroma dataset.
>> idxN <- which(infoSamples$type=="Normal");
>> idxT <- which(infoSamples$type=="Tumor");
>
> This is a bit dangerous since it assumes that the rows in your
> 'samples.txt' file is ordered the same way as the files on this. At
> least I would assert that that is the case by something like:
>
> stopifnot(all(infoSamples$name == getName(dsC));
>
> or similar.
>
>> dsN <- extract(dsC, idxN);
>> dsT <- extract(dsC, idxT);
>> # Circular binary segmentation T vs N: Paired model (first N sample pairs
>> with first T sample)
>> cns <- CbsModel(dsT, dsN);
>> fit(cns, verbose=TRUE);
>> regDatList <- getRegions(cns);
>
> Yes, this does a tumor-normal paired CBS segmentation (and extracts
> the table of regions afterward).
>
>> # Circular binary segmentation T vs N: Unpaired: I DON'T KNOW IF THIS IS
>> CORRECT (cns.unpaired keeps me telling that the reference sample is made of
>> 102 files instead of one!).
>> avgN <- getAverageFile(dsN);
>
> This is the correct command and 'avgN' should *indeed* a single file
> ("array") here. You should be able verify by looking at what:
>
> print(avgN);
>
> returns.
>
>> cns.unpaired <- CbsModel(dsT, avgN);
>
> This should work, because 'dsT' is a data set; verify by
>
> print(dsT);
>
> If it doesn't work please let us know what:
>
> print(dsT);
> print(avgN);
>
> returns and what the complete error message is.
>
>> fit(cns.unpaired, verbose=TRUE);
>> regDatList.unpaired <- getRegions(cns.unpaired);
I forgot to add that you should find the recent thread 'Combine paired
and unpaired CN analysis' (started on May 23, 2001) useful:
https://groups.google.com/forum/#!topic/aroma-affymetrix/220dWcCxxn8
/Henrik
>
> [snip]
>
> I'll answer your second question in a separate thread ...and when I
> find the time.
>
> /Henrik
>
>> Thank you very much for your help!
>> Best,
>> Xavi.
>> #SESSION INFO
>>> sessionInfo()
>> R version 2.13.0 (2011-04-13)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> locale:
>> [1] C
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>> other attached packages:
>> [1] DNAcopy_1.26.0 aroma.cn_0.5.2 aroma.affymetrix_2.1.0
>> [4] aroma.apd_0.1.8 affxparser_1.24.0 R.huge_0.2.2
>> [7] aroma.core_2.1.0 aroma.light_1.20.0 matrixStats_0.2.2
>> [10] R.rsp_0.5.3 R.cache_0.4.2 R.filesets_1.0.1
>> [13] digest_0.5.0 R.utils_1.7.5 R.oo_1.8.0
>> [16] R.methodsS3_1.2.1
>> loaded via a namespace (and not attached):
>> [1] tools_2.13.0
>>
>> --
>> 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/
>>
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo()
Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Hi.
On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole wrote:
> Hi all,
> I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I
> have tumor and normal samples, and now I want to apply an unpaired CBS
> model. I know ho to do the paired model, but I'm not sure is this code is
> right for the unpaired one:
> library(aroma.affymetrix);
> library(aroma.cn);
No need for 'aroma.cn' here.
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
> options(digits=4);
> setOption(aromaSettings, "memory/ram", 500.0)
> # Verify that the data set can be located:
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> dataSet <- "CEL_files";
Each analysis you run should have a unique data set name, i.e. what
name should you use next time? I recommend to use a much more
informative name of your data set - something that reflects the
project name and/or the investigator and the year, or similar.
> dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
> setFullName(dsR, dataSet);
No need to do this.
> # Using CRMAv2
> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
Since you've already have setup an AffymetrixCelSet object ('dsR')
above, you should use that instead:
dsList <- doCRMAv2(dsR, combineAlleles=FALSE, verbose=verbose);
or even shorter for allele-specific analysis, you can equivalently do:
dsList <- doASCRMAv2(dsR, verbose=verbose);
> dsC <- dsList$total;
> # Splitting the dataset in normal-tumor pairs
> infoSamples <- read.table("samples.txt", sep="\t", header=TRUE, as.is=TRUE,
> strip.white=TRUE);
> #Rows in this file are in the same order as arrays in the aroma dataset.
> idxN <- which(infoSamples$type=="Normal");
> idxT <- which(infoSamples$type=="Tumor");
This is a bit dangerous since it assumes that the rows in your
'samples.txt' file is ordered the same way as the files on this. At
least I would assert that that is the case by something like:
stopifnot(all(infoSamples$name == getName(dsC));
or similar.
> dsN <- extract(dsC, idxN);
> dsT <- extract(dsC, idxT);
> # Circular binary segmentation T vs N: Paired model (first N sample pairs
> with first T sample)
> cns <- CbsModel(dsT, dsN);
> fit(cns, verbose=TRUE);
> regDatList <- getRegions(cns);
Yes, this does a tumor-normal paired CBS segmentation (and extracts
the table of regions afterward).
> # Circular binary segmentation T vs N: Unpaired: I DON'T KNOW IF THIS IS
> CORRECT (cns.unpaired keeps me telling that the reference sample is made of
> 102 files instead of one!).
> avgN <- getAverageFile(dsN);
This is the correct command and 'avgN' should *indeed* a single file
("array") here. You should be able verify by looking at what:
print(avgN);
returns.
> cns.unpaired <- CbsModel(dsT, avgN);
This should work, because 'dsT' is a data set; verify by
print(dsT);
If it doesn't work please let us know what:
print(dsT);
print(avgN);
returns and what the complete error message is.
> fit(cns.unpaired, verbose=TRUE);
> regDatList.unpaired <- getRegions(cns.unpaired);
[snip]
I'll answer your second question in a separate thread ...and when I
find the time.
/Henrik
> Thank you very much for your help!
> Best,
> Xavi.
> #SESSION INFO
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> locale:
> [1] C
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] DNAcopy_1.26.0 aroma.cn_0.5.2 aroma.affymetrix_2.1.0
> [4] aroma.apd_0.1.8 affxparser_1.24.0 R.huge_0.2.2
> [7] aroma.core_2.1.0 aroma.light_1.20.0 matrixStats_0.2.2
> [10] R.rsp_0.5.3 R.cache_0.4.2 R.filesets_1.0.1
> [13] digest_0.5.0 R.utils_1.7.5 R.oo_1.8.0
> [16] R.methodsS3_1.2.1
> loaded via a namespace (and not attached):
> [1] tools_2.13.0
>
> --
> 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/
>
--
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/
[aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
Hi all,
I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I
have tumor and normal samples, and now I want to apply an unpaired CBS
model. I know ho to do the paired model, but I'm not sure is this code is
right for the unpaired one:
library(aroma.affymetrix);
library(aroma.cn);
verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
options(digits=4);
setOption(aromaSettings, "memory/ram", 500.0)
# Verify that the data set can be located:
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
dataSet <- "CEL_files";
dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
setFullName(dsR, dataSet);
# Using CRMAv2
dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
dsC <- dsList$total;
# Splitting the dataset in normal-tumor pairs
infoSamples <- read.table("samples.txt", sep="\t", header=TRUE, as.is=TRUE,
strip.white=TRUE);
#Rows in this file are in the same order as arrays in the aroma dataset.
idxN <- which(infoSamples$type=="Normal");
idxT <- which(infoSamples$type=="Tumor");
dsN <- extract(dsC, idxN);
dsT <- extract(dsC, idxT);
# Circular binary segmentation T vs N: Paired model (first N sample pairs
with first T sample)
cns <- CbsModel(dsT, dsN);
fit(cns, verbose=TRUE);
regDatList <- getRegions(cns);
# Circular binary segmentation T vs N: Unpaired: I DON'T KNOW IF THIS IS
CORRECT (cns.unpaired keeps me telling that the reference sample is made of
102 files instead of one!).
avgN <- getAverageFile(dsN);
cns.unpaired <- CbsModel(dsT, avgN);
fit(cns.unpaired, verbose=TRUE);
regDatList.unpaired <- getRegions(cns.unpaired);
Besides that, another doubt I have is how to extract raw total copy numbers
into a tab-delimited file after applying doCRMA. Is this code correct? I
assume these CN values are normalized, aren't they?
dataSet <- "CEL_files";
tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY";
chipType <- "GenomeWideSNP_6";
ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
chipType=chipType);
dfTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome", "position",
"*"));
print(dfTxt);
If I wanted to extract allele-specific CN is it enough to change
tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY";
to
tags <- "ACC,ra,-XY,BPN,-XY,A+B,FLN,-XY";
?
Thank you very much for your help!
Best,
Xavi.
#SESSION INFO
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.26.0 aroma.cn_0.5.2 aroma.affymetrix_2.1.0
[4] aroma.apd_0.1.8affxparser_1.24.0 R.huge_0.2.2
[7] aroma.core_2.1.0 aroma.light_1.20.0 matrixStats_0.2.2
[10] R.rsp_0.5.3R.cache_0.4.2 R.filesets_1.0.1
[13] digest_0.5.0 R.utils_1.7.5 R.oo_1.8.0
[16] R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.13.0
--
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/
