On Tue, Mar 8, 2011 at 8:02 AM, Oscar Rueda <oscar.ru...@cancer.org.uk> wrote:
> Thanks a lot, Henrik.
>
> Wouldn¹t it be
>
>> a <- fit[[1]]$fitValleys$x[1];
>> b <- fit[[1]]$fitValleys$x[2];

Corrected.

>
>
> I have one more question. Now I¹m getting to the TumorBoost normalization
> and I¹m following the vignette. I have several batches of paired samples. In
> this particular one, I have 98 samples (49 tumours and 49 normals).
>
> So I create my list:
>
>> dsList <- list(normal=dsN, tumor=dsT, callsN=gsN);
>> print(dsList)
>
> $normal
> AromaUnitFracBCnBinarySet:
> Name: MatchedPairs1
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Full name: MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Number of files: 49
> Names: A430-019, A430-020, ..., A488-1563 [49]
> Path (to the first file):
> totalAndFracBData/MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP
> _6
> Total file size: 351.70 MB
> RAM: 0.07MB
>
> $tumor
> AromaUnitFracBCnBinarySet:
> Name: MatchedPairs1
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Full name: MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Number of files: 49
> Names: A430-007, A430-008, ..., A488-2631 [49]
> Path (to the first file):
> totalAndFracBData/MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP
> _6
> Total file size: 351.70 MB
> RAM: 0.07MB
>
> $callsN
> AromaUnitGenotypeCallSet:
> Name: MatchedPairs1
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC
> Full name: MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC
> Number of files: 49
> Names: A430-017, A430-019, ..., A488-2630 [49]
> Path (to the first file):
> callData/MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC/GenomeWideSNP_6
> Total file size: 175.85 MB
> RAM: 0.07MB
>
>
> The samples are sorted in order to form pairs.
>
> But when I try to the run the next lines of the vignette I get a warning and
> my object losses the tumours:
>
>> dsList <- lapply(dsList, FUN=function(ds) {
>>   idxs <- indexOf(ds, getNames(dsList$normal));
>>   extract(ds, idxs);
>> });
>> print(dsList);

This is a reordering of the three data sets to make sure that the k:th
array in each set correspond to the same sample/patient.  I've
clarified this in the vignette:

  http://aroma-project.org/vignettes/tumorboost-highlevel

If you have already ordered your arrays in a different way, you can
skip this step.

Hope this helps

/Henrik
>
>> + + + Warning messages:
> 1: In min(x) : no non-missing arguments to min; returning Inf
> 2: In max(x) : no non-missing arguments to max; returning -Inf
>> $normal
> AromaUnitFracBCnBinarySet:
> Name: MatchedPairs1
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Full name: MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> Number of files: 49
> Names: A430-019, A430-020, ..., A488-1563 [49]
> Path (to the first file):
> totalAndFracBData/MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP
> _6
> Total file size: 351.70 MB
> RAM: 0.07MB
>
> $tumor
> AromaUnitFracBCnBinarySet:
> Name: NA
> Full name: NA
> Number of files: 49
> Names: NA, NA, ..., NA [49]
> Path (to the first file): NA
> Total file size: NA MB
> RAM: 0.07MB
>
> $callsN
> AromaUnitGenotypeCallSet:
> Name: MatchedPairs1
> Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC
> Full name: MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC
> Number of files: 49
> Names: A430-019, A430-020, ..., A488-1563 [49]
> Path (to the first file):
> callData/MatchedPairs1,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC/GenomeWideSNP_6
> Total file size: 175.85 MB
> RAM: 0.07MB
>
> It seems it can't find the names of the normal samples in the names of the
> tumour samples, but I don't understand what are those lines for.
> I've also noticed that in the vignette there are only one pair of samples.
> Do I have to run each pair in a loop?
>
> Thanks again for your input.
>
> Cheers,
> Oscar
>
> On 7/3/11 23:26, "Henrik Bengtsson" <henrik.bengts...@aroma-project.org>
> wrote:
>
>> Thanks for pointing this out.  I've updated the vignette to:
>>
>> a <- fit$fitValleys$x[1];
>> b <- fit$fitValleys$x[2];
>>
>> /H
>>
>> On Mon, Mar 7, 2011 at 5:28 AM, Oscar Rueda <oscar.ru...@cancer.org.uk> 
>> wrote:
>>> Thanks a lot, Henrik!
>>>
>>> This has solved my problem.
>>> One more thing about the vignette: the code to call for confidence scores
>>> does not work for me:
>>>
>>>> a <- fit$x[1];
>>>> b <- fit$x[2];
>>>> cs[isDiploid] <- rowMins(abs(cbind(betaN[isDiploid]-a,
>>>> betaN[isDiploid]-b)));
>>>
>>>>> Error in cs[isDiploid] <- rowMins(abs(cbind(betaN[isDiploid] - a,
>>> betaN[isDiploid] -  :
>>>  replacement has length zero
>>>
>>> The object fit I get looks like this:
>>>
>>>> fit
>>> [[1]]
>>> [[1]]$cn
>>> [1] 2
>>>
>>> [[1]]$nbrOfGenotypeGroups
>>> [1] 3
>>>
>>> [[1]]$fit
>>>    type         x   density
>>> 1   peak 0.1228705 1.5184897
>>> 2 valley 0.3286780 0.5909177
>>> 3   peak 0.4792689 1.1727220
>>> 4 valley 0.6348794 0.5681927
>>> 5   peak 0.8356672 1.4166525
>>>
>>> [[1]]$fitValleys
>>>    type         x   density
>>> 2 valley 0.3286780 0.5909177
>>> 4 valley 0.6348794 0.5681927
>>>
>>> [[1]]$n
>>> [1] 934063
>>>
>>>
>>> attr(,"class")
>>> [1] "NaiveGenotypeModelFit" "list"
>>>
>>> So there is no fit$x element. Anyway, I don't think I need these confidence
>>> scores for TumourBoost.
>>>
>>> Cheers,
>>> Oscar
>>>
>>>
>>> On 4/3/11 05:05, "Henrik Bengtsson" <henrik.bengts...@aroma-project.org>
>>> wrote:
>>>
>>>> Hi again,
>>>>
>>>> after receiving your data I could (i) reproduce the problem, and more
>>>> importantly (ii) fix the bug causing it.  The reason was, as you
>>>> concluded, that in findPeaksAndValleys(x, to), when 'x' is a numeric,
>>>> argument 'to' was interpreted via partial argument matching as the
>>>> 'tol' argument instead of being passed on to density() via arguments
>>>> '...'.  This was easily corrected by changing the order of 'tol' and
>>>> '...' from:
>>>>
>>>> findPeaksAndValleys.numeric <- function(x, tol=0, ..., na.rm=TRUE)
>>>>
>>>> to
>>>>
>>>> findPeaksAndValleys.numeric <- function(x, ..., tol=0, na.rm=TRUE)
>>>>
>>>> With your data, this simple fix will give the correct gender call with
>>>> and without argument 'to', i.e.
>>>>
>>>>> callXXorXY(betaN[is23], betaN[is24])
>>>> [1] "XX"
>>>>> callXXorXY(betaN[is23], betaN[is24], from=0, to=1)
>>>> [1] "XX"
>>>>
>>>>
>>>> I've committed the bug fix to aroma.light v1.18.4 (BioC release) as
>>>> well as aroma.light v1.19.4 (BioC devel).  Until it's available there,
>>>> you can also install it from source by:
>>>>
>>>> source("http://aroma-project.org/hbLite.R";);
>>>> installPackages("http://www.braju.com/R/repos/aroma.light_1.18.4.tar.gz";) ;
>>>>
>>>>
>>>> Thanks.
>>>>
>>>> /Henrik
>>>>
>>>> On Mon, Feb 28, 2011 at 12:07 PM, Henrik Bengtsson
>>>> <henrik.bengts...@aroma-project.org> wrote:
>>>>> Y8l
>>>>>
>>>>> On Mon, Feb 28, 2011 at 4:09 AM, Oscar Rueda <oscar.ru...@cancer.org.uk>
>>>>> wrote:
>>>>>> HI,
>>>>>> Thanks for your answer.
>>>>>> I¹ve updated the packages, and I don¹t get the error in callXXorXY()
>>>>>> anymore.
>>>>>
>>>>> Good.
>>>>>
>>>>>> But I guess the problem with the arguments Ofrom¹ and Oto¹ is still
>>>>>> there:
>>>>>>
>>>>>>> callXXorXY(betaN[is23], betaN[is24], adjust=adjust, from=0, to=1);
>>>>>> [1] "XY"
>>>>>>> callXXorXY(betaN[is23], betaN[is24], adjust=adjust)
>>>>>> [1] "XX"
>>>>>>
>>>>>> When I try to run
>>>>>>
>>>>>>>   isDiploid <- (!(is23 | is24));
>>>>>>>
>>>>>>>   use <- which(isDiploid);
>>>>>>>
>>>>>>>   muT <- callNaiveGenotypes(betaN[use], cn=2, adjust=adjust, from=0,
>>>>>>> to=1,
>>>>>>>
>>>>>>>                                         verbose=less(verbose,10));
>>>>>>>
>>>>>>
>>>>>> I get
>>>>>>
>>>>>>>> + Error: nbrOfGenotypeGroups == 3 is not TRUE
>>>>>>>>
>>>>>>
>>>>>>
>>>>>> I know that this sample is female, so my guess is that Oto=1¹ gets a
>>>>>> partial
>>>>>> match with Otol¹ when passed to findPeaksAndValleys.density() and deletes
>>>>>> any peaks and valleys with density smaller than 1.
>>>>>
>>>>> Sorry, I missed your important point that arguments 'to' and 'tol' get
>>>>> mixed up; that's not good.   Thanks for bringing it up again.  I'll
>>>>> look into it.  I'd also like to be able to reproduce exactly what
>>>>> you're getting.  Would you mind fwd your data to me (you can do it
>>>>> offline)?  The following should do:
>>>>>
>>>>>  saveObject(list(betaN=betaN, is23=is23, is24=is24),
>>>>> "RuedaO_20110228,callXXorXY.RData");
>>>>>
>>>>> FYI, censoring/setting the range of the density estimate with 'to=0'
>>>>> and 'from=1' is slightly controversial because the BAFs can indeed be
>>>>> slightly outside [0,1] as well.  This is because we allow for
>>>>> (slightly) negative (CA,CB) estimates.  However, since the BAFs will
>>>>> only be slightly outside [0,1] I don't think this is a big issue (but
>>>>> it hasn't been fully investigated).
>>>>>
>>>>> Thxs
>>>>>
>>>>> /Henrik
>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>> Oscar
>>>>>>
>>>>>> On 27/2/11 23:41, "Henrik Bengtsson" <henrik.bengts...@aroma-project.org>
>>>>>> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> thanks for reporting on this.  Before doing anything else, try with
>>>>>> aroma.cn to v0.5.2;
>>>>>>
>>>>>> source("http://aroma-project.org/hbLite.R";);
>>>>>> hbInstall("aroma.cn");
>>>>>>
>>>>>>
>>>>>> From its NEWS file:
>>>>>>
>>>>>> Version: 0.5.2 [2010-08-04]
>>>>>> o Added option 'preserveScale' to TumorBoostNormalization for
>>>>>>   correcting for signal compression in heterozygous SNPs.
>>>>>>   The defaults is to do this correction.
>>>>>>
>>>>>> Version: 0.5.1 [2010-07-25]
>>>>>> o callXXorXY() no longer calls gender from chr Y when gender is
>>>>>>   estimated as 'XX' from chr X.
>>>>>>
>>>>>> So, we actually made a change to the internal callXXorXY() that should
>>>>>> address the problems you are experiencing.
>>>>>>
>>>>>> Try to see if the above version solves your problem - if not, please
>>>>>> let us know again.
>>>>>>
>>>>>> /Henrik
>>>>>>
>>>>>> PS. aroma.cn v0.5.2 is actually a version from Aug 2010 that I forgot
>>>>>> to make publicly available; I've just uploaded to CRAN too.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Feb 23, 2011 at 9:34 AM, Oscar Rueda <oscar.ru...@cancer.org.uk>
>>>>>> wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I'm trying to run TumorBoost on a set of matched pairs. Like the 
>>>>>>> vignette
>>>>>>> suggests, I have first run
>>>>>>>
>>>>>>> ds <- doASCRMAv2("TCGA,GBM", chipType="GenomeWideSNP_6,Full");
>>>>>>>
>>>>>>> Then I'm doing the naïve genotyping following all the steps in the
>>>>>>> vignette.
>>>>>>> But when I try to get the gender I get the following error
>>>>>>>
>>>>>>>> gender <- callXXorXY(betaN[is23], betaN[is24], adjust=adjust, from=0,
>>>>>>>> to=1);
>>>>>>> Error in list(`callXXorXY(betaN[is23], betaN[is24], adjust = adjust, 
>>>>>>> from
>>>>>>> =
>>>>>>> 0,
>>>>>>> to = 1)` = <environment>,  :
>>>>>>>
>>>>>>> [2011-02-23 16:22:05] Exception: Allele B fractions for ChrX and ChrY 
>>>>>>> are
>>>>>>> inconsistent.
>>>>>>>  at throw(Exception(...))
>>>>>>>  at throw.default("Allele B fractions for ChrX and ChrY are
>>>>>>> inconsistent.")
>>>>>>>  at throw("Allele B fractions for ChrX and ChrY are inconsistent.")
>>>>>>>  at callXXorXY.numeric(betaN[is23], betaN[is24], adjust = adjust, from =
>>>>>>> 0,
>>>>>>> to
>>>>>>>  at callXXorXY(betaN[is23], betaN[is24], adjust = adjust, from = 0, to =
>>>>>>> 1)
>>>>>>>
>>>>>>> I know that my samples are female, so I can set manually
>>>>>>>> gender <- "XX"
>>>>>>>
>>>>>>> But then I try to run the naïve genotyping and get another error:
>>>>>>>
>>>>>>>> muT <- callNaiveGenotypes(betaN[use], cn=2, adjust=adjust, from=0, 
>>>>>>>> to=1,
>>>>>>>                                        verbose=less(verbose,10));
>>>>>>>
>>>>>>>>> + Error: nbrOfGenotypeGroups == 3 is not TRUE
>>>>>>>
>>>>>>>
>>>>>>> Taking a look at both errors I've seen that they come from the same
>>>>>>> function,
>>>>>>>
>>>>>>>  fit <- findPeaksAndValleys(yT, adjust = adjust, ...)
>>>>>>>
>>>>>>> This function works OK if run directly on the BAFs of chromosome X 
>>>>>>> (finds
>>>>>>> 3
>>>>>>> valleys and their peaks) but when we pass the argument 'from' and 'to',
>>>>>>> the
>>>>>>> argument 'to' is mistaken with argument 'tol', and as
>>>>>>> findPeaksAndValleys.density() does at the end
>>>>>>>
>>>>>>>>    if (tol > 0) {
>>>>>>>>        res <- subset(res, density >= tol)
>>>>>>>>    }
>>>>>>>
>>>>>>>
>>>>>>> I don't get 3 peaks and 2 valleys anymore, but just 2 peaks (the ones
>>>>>>> with
>>>>>>> density values larger than 1). And the function returns the
>>>>>>> aforementioned
>>>>>>> error.
>>>>>>>
>>>>>>> So my question is; is it OK to run  callXXorXY() and 
>>>>>>> callNaiveGenotypes()
>>>>>>> removing the arguments 'from' and 'to'?
>>>>>>>
>>>>>>> My sessionInfo is:
>>>>>>>
>>>>>>>> sessionInfo()
>>>>>>> R version 2.12.0 (2010-10-15)
>>>>>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>>>>>
>>>>>>> locale:
>>>>>>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>>>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>>>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>>>>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>>>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>>>>
>>>>>>> attached base packages:
>>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>>
>>>>>>> other attached packages:
>>>>>>>  [1] aroma.cn_0.5.0     aroma.core_2.0.0   aroma.light_1.18.3
>>>>>>> matrixStats_0.2.2
>>>>>>>  [5] R.rsp_0.4.2        R.filesets_0.9.2   digest_0.4.2
>>>>>>> R.cache_0.4.0
>>>>>>>  [9] R.utils_1.6.2      R.oo_1.7.5         R.methodsS3_1.2.1
>>>>>>>
>>>>>>> loaded via a namespace (and not attached):
>>>>>>> [1] affxparser_1.22.0
>>>>>>>>
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>> Oscar
>>>>>>>
>>>>>>>
>>>>>>> Oscar M. Rueda, PhD.
>>>>>>> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
>>>>>>> Cancer Research UK Cambridge Research Institute.
>>>>>>> Li Ka Shing Centre, Robinson Way.
>>>>>>> Cambridge CB2 0RE
>>>>>>> England
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> This communication is from Cancer Research UK. Our website is at
>>>>>>> www.cancerresearchuk.org. We are a registered charity in England and
>>>>>>> Wales
>>>>>>> (1089464) and in Scotland (SC041666) and a company limited by guarantee
>>>>>>> registered in England and Wales under number 4325234. Our registered
>>>>>>> address
>>>>>>> is Angel Building, 407 St John Street, London, EC1V 4AD. Our central
>>>>>>> telephone number is 020 7242 0200.
>>>>>>>
>>>>>>> This communication and any attachments contain information which is
>>>>>>> confidential and may also be privileged.   It is for the exclusive use 
>>>>>>> of
>>>>>>> the intended recipient(s).  If you are not the intended recipient(s)
>>>>>>> please
>>>>>>> note that any form of disclosure, distribution, copying or use of this
>>>>>>> communication or the information in it or in any attachments is strictly
>>>>>>> prohibited and may be unlawful.  If you have received this communication
>>>>>>> in
>>>>>>> error, please notify the sender and delete the email and destroy any
>>>>>>> copies
>>>>>>> of it.
>>>>>>>
>>>>>>> E-mail communications cannot be guaranteed to be secure or error free, 
>>>>>>> as
>>>>>>> information could be intercepted, corrupted, amended, lost, destroyed,
>>>>>>> arrive late or incomplete, or contain viruses.  We do not accept
>>>>>>> liability
>>>>>>> for any such matters or their consequences.  Anyone who communicates 
>>>>>>> with
>>>>>>> us
>>>>>>> by e-mail is taken to accept the risks in doing so.
>>>>>>>
>>>>>>> --
>>>>>>> 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/
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Oscar M. Rueda, PhD.
>>>>>> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
>>>>>> Cancer Research UK Cambridge Research Institute.
>>>>>> Li Ka Shing Centre, Robinson Way.
>>>>>> Cambridge CB2 0RE
>>>>>> England
>>>>>>
>>>>>>
>>>>>>
>>>>>> This communication is from Cancer Research UK. Our website is at
>>>>>> www.cancerresearchuk.org. We are a registered charity in England and 
>>>>>> Wales
>>>>>> (1089464) and in Scotland (SC041666) and a company limited by guarantee
>>>>>> registered in England and Wales under number 4325234. Our registered
>>>>>> address
>>>>>> is Angel Building, 407 St John Street, London, EC1V 4AD. Our central
>>>>>> telephone number is 020 7242 0200.
>>>>>>
>>>>>> This communication and any attachments contain information which is
>>>>>> confidential and may also be privileged. It is for the exclusive use of
>>>>>> the
>>>>>> intended recipient(s). If you are not the intended recipient(s) please
>>>>>> note
>>>>>> that any form of disclosure, distribution, copying or use of this
>>>>>> communication or the information in it or in any attachments is strictly
>>>>>> prohibited and may be unlawful. If you have received this communication 
>>>>>> in
>>>>>> error, please notify the sender and delete the email and destroy any
>>>>>> copies
>>>>>> of it.
>>>>>>
>>>>>> E-mail communications cannot be guaranteed to be secure or error free, as
>>>>>> information could be intercepted, corrupted, amended, lost, destroyed,
>>>>>> arrive late or incomplete, or contain viruses. We do not accept liability
>>>>>> for any such matters or their consequences. Anyone who communicates with
>>>>>> us
>>>>>> by e-mail is taken to accept the risks in doing so.
>>>>>>
>>>>>> --
>>>>>> 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/
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> Oscar M. Rueda, PhD.
>>> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
>>> Cancer Research UK Cambridge Research Institute.
>>> Li Ka Shing Centre, Robinson Way.
>>> Cambridge CB2 0RE
>>> England
>>>
>>>
>>>
>>>
>>> This communication is from Cancer Research UK. Our website is at
>>> www.cancerresearchuk.org. We are a registered charity in England and Wales
>>> (1089464) and in Scotland (SC041666) and a company limited by guarantee
>>> registered in England and Wales under number 4325234. Our registered address
>>> is Angel Building, 407 St John Street, London, EC1V 4AD. Our central
>>> telephone number is 020 7242 0200.
>>>
>>> This communication and any attachments contain information which is
>>> confidential and may also be privileged.   It is for the exclusive use of 
>>> the
>>> intended recipient(s).  If you are not the intended recipient(s) please note
>>> that any form of disclosure, distribution, copying or use of this
>>> communication or the information in it or in any attachments is strictly
>>> prohibited and may be unlawful.  If you have received this communication in
>>> error, please notify the sender and delete the email and destroy any copies
>>> of it.
>>>
>>> E-mail communications cannot be guaranteed to be secure or error free, as
>>> information could be intercepted, corrupted, amended, lost, destroyed, 
>>> arrive
>>> late or incomplete, or contain viruses.  We do not accept liability for any
>>> such matters or their consequences.  Anyone who communicates with us by
>>> e-mail is taken to accept the risks in doing so.
>>>
>>
>
>
> Oscar M. Rueda, PhD.
> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
> Cancer Research UK Cambridge Research Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
> England
>
>
>
>
> This communication is from Cancer Research UK. Our website is at 
> www.cancerresearchuk.org. We are a registered charity in England and Wales 
> (1089464) and in Scotland (SC041666) and a company limited by guarantee 
> registered in England and Wales under number 4325234. Our registered address 
> is Angel Building, 407 St John Street, London, EC1V 4AD. Our central 
> telephone number is 020 7242 0200.
>
> This communication and any attachments contain information which is 
> confidential and may also be privileged.   It is for the exclusive use of the 
> intended recipient(s).  If you are not the intended recipient(s) please note 
> that any form of disclosure, distribution, copying or use of this 
> communication or the information in it or in any attachments is strictly 
> prohibited and may be unlawful.  If you have received this communication in 
> error, please notify the sender and delete the email and destroy any copies 
> of it.
>
> E-mail communications cannot be guaranteed to be secure or error free, as 
> information could be intercepted, corrupted, amended, lost, destroyed, arrive 
> late or incomplete, or contain viruses.  We do not accept liability for any 
> such matters or their consequences.  Anyone who communicates with us by 
> e-mail is taken to accept the risks in doing so.
>

-- 
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version of the package, 2) to report the output of sessionInfo() and 
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