Re: [aroma.affymetrix] Unpaired copy number analysis with doCRMAv2
On Fri, Jun 17, 2011 at 12:15 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi.
On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole xavier.s...@gmail.com 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.
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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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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 henrik.bengts...@aroma-project.org
Hi.
On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole xavier.s...@gmail.com 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(), 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
