Hi.
On Thu, Oct 2, 2008 at 2:39 AM, marco <[EMAIL PROTECTED]> wrote:
>
> Dear Henrik,
>
> I tried the X chromosome variant but I am not sure I can het it to
> work.
> I made a *.saf file and place it into annotationData/samples/
> File looks like this:
>
> name:MD10
> tags:XY
> name:MD11
> tags:XY
> name:MD12
> tags:XY
> name:MD13
> ...
> ...
This looks correct to me. Maybe you should try to add an empty line
between the entries. What is the full filename of this file?
>
> Anyway I cannot get the function getAttributes to work, so I am unsure
> if the *.saf is read correctly.
> Below is the output:
>> cdf <- AffymetrixCdfFile$fromChipType("GenomeWideSNP_6", tags="Full")
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>> gi <- getGenomeInformation(cdf)
>> print(gi)
> UgpGenomeInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na24,HB20080214
> Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,Full,na24,HB20080214.ugp
> File size: 8.97MB
> RAM: 0.00MB
> Chip type: GenomeWideSNP_6,Full
>> si <- getSnpInformation(cdf)
>> print(si)
> UflSnpInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na24,HB20080214
> Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> GenomeWideSNP_6,Full,na24,HB20080214.ufl
> File size: 7.18MB
> RAM: 0.00MB
> Chip type: GenomeWideSNP_6,Full
> Number of enzymes: 2
>> cs <- AffymetrixCelSet$fromName("ESC", cdf=cdf)
If you do
cs <- AffymetrixCelSet$fromName("ESC", cdf=cdf, verbose=-20)
You should see from the output showing what SAF files are located and
that they are read, e.g.
cdf <- AffymetrixCdfFile$byChipType("Mapping50K_Hind240");
csR <- AffymetrixCelSet$byName("HapMap270,100K,CEU,testSet", cdf=cdf,
verbose=-20);
...
20081004 16:47:49| Allocating a new AffymetrixCelSet instance...done
20081004 16:47:49| Updating newly allocated AffymetrixCelSet...
20081004 16:47:49| Updating AffymetrixCelSet...
20081004 16:47:49| Scanning for and applying sample annotation files...
SampleAnnotationSet:
Name: annotationData
Tags:
Full name: annotationData
Number of files: 7
Names: 000.default, AGRF_2007a, ..., HapMap270
Path (to the first file): annotationData/samples
Total file size: 0.03MB
RAM: 0.00MB
20081004 16:47:50| Scanning for and applying sample annotation files...done
20081004 16:47:50| Updating AffymetrixCelSet...done
20081004 16:47:50| Updating newly allocated AffymetrixCelSet...done
20081004 16:47:50| Defining an AffymetrixCelSet object from files...done
...
>> print(cs)
> AffymetrixCelSet:
> Name: ESC
> Tags:
> Path: rawData/ESC/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> Number of arrays: 26
> Names: MD10, MD11, ..., VT06_TER2102EP
> Time period: 2008-07-11 11:09:02 -- 2008-09-03 14:47:43
> Total file size: 1712.75MB
> RAM: 0.04MB
>> cf <- getFile(cs, indexOf(cs, "MD10"));
> AffymetrixCelFile:
> Name: MD10
> Tags:
> Pathname: rawData/ESC/GenomeWideSNP_6/MD10.CEL
> File size: 65.88MB
> RAM: 0.01MB
> File format: v1 (binary; CC)
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> Timestamp: 2008-07-17 19:31:03
>> attrs <- getAttributes(cf);
> Error in order(names(attrs)) : argument 1 is not a vector
This does indeed indicate that there were no attributes set, i.e. it
looks like the *.saf file was not located. (In next release, this
will return NULL instead of giving an error).
Did the above help?
/Henrik
>> sessionInfo()
>
> R version 2.7.2 (2008-08-25)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods
> base
>
> other attached packages:
> [1] aroma.affymetrix_0.9.4 aroma.apd_0.1.3
> R.huge_0.1.6
> [4] affxparser_1.12.2 aroma.core_0.9.4
> sfit_0.1.5
> [7] aroma.light_1.8.1 digest_0.3.1
> matrixStats_0.1.3
> [10] R.rsp_0.3.4 R.cache_0.1.7
> R.utils_1.0.4
> [13] R.oo_1.4.6 R.methodsS3_1.0.3
>
>
> Best Regards
>
> Marco
>
>
>
>
>
>
> On Sep 19, 10:10 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]>
> wrote:
>> Hi.
>>
>> On Fri, Sep 19, 2008 at 4:35 AM, marco <[EMAIL PROTECTED]> wrote:
>>
>> > Dear List,
>>
>> > I wonder about how X chromosome is treated in aroma.affymetrix.
>> > Is the mix of male/female samples somehow taken into account, or X is
>> > processed as any other chromosome?
>>
>> Good idea ;) Yes, the CRMA model does take into account the fact
>> that different samples have different ploidies on ChrX when using the
>> pool of arrays as a reference. The idea is to calculate the robust
>> average across all arrays and correct for the bias that
>> non-copy-neutral samples introduce. See Section '3.2.7 Reference
>> signals' in:
>>
>> H. Bengtsson; R. Irizarry; B. Carvalho; T. Speed, Estimation and
>> assessment of raw copy numbers at the single locus level,
>> Bioinformatics, 2008. [pmid: 18204055] [doi:
>> 10.1093/bioinformatics/btn016]
>>
>> for more details. The model/method requires that at least one sample
>> is copy neutral, i.e. you need at least one "female" in order to
>> estimate a diploid reference on ChrX. The same bias-correction
>> method can also be used when some of samples are say trisomy 21. For
>> ChrY, our current model cannot give you a *diploid* ChrY reference,
>> but a *copy neutral* one, i.e. CN=1 (requires at least one "male").
>> To the best of my understand, none of the other methods out there use
>> this, but instead it is common to see that only female samples are
>> used for the ChrX reference. See the above CRMA paper to see how much
>> the ChrX CN estimates are improved when you use the above
>> bias-corrected method instead.
>>
>>
>>
>> > In these case the female and males test array are supposed to have
>> > log2 values on the average over and below zero?
>>
>> I'm note sure what you mean by this, but maybe the above answered this
>> question too.
>>
>> So, how do you do this in aroma.affymetrix? I have on purpose avoided
>> giving the details on this until someone asks for it, because it
>> involved the use of a new kind of non-finalized sample annotation
>> files (SAFs). I don't want to bother people with alpha versions in
>> case the API/format changes. It is unlikely that it will change much
>> but if you can accept that it might change, I created a new vignette
>> explaining how to do it:
>>
>> Vignette 'Sex-chromosome bias-corrected reference signals from pooled
>> average'http://groups.google.com/group/aroma-affymetrix/web/sex-chromosome-bi...
>>
>> It also illustrated a lot of other things so it might be useful for others
>> too.
>>
>> Hope this helps
>>
>> Henrik
>>
>>
>>
>> > Regards
>>
>> > Marco
> >
>
--~--~---------~--~----~------------~-------~--~----~
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.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
