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. > -- 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/