Everything goes very well. Nsp and Sty matched.

BUT I forget to ask in which step should I pair the samples with tumor and 
normal. According to , Vignette: Paired total copy-number analysis
cns <- CbsModel(dsT, dsN)

now I am using doCBS, how can I connect to the above step?

Many thanks,

Wei


On Wednesday, June 5, 2013 5:50:52 PM UTC-4, Henrik Bengtsson wrote:
>
> JOn Wed, Jun 5, 2013 at 2:15 PM, Wei Tang <tangw...@gmail.com<javascript:>> 
> wrote: 
> > do they need to be the same names in 500K? How about SNP5, they are 
> > additional samples. 
>
> Yes (I did write this in my long initial message).  doCBS() identifies 
> which tuples of arrays belongs to which samples by matching up their 
> *names*, that is, by looking at: 
>
> getNames(dsC_EC500K_Nsp) 
> getNames(dsC_EC500K_Sty) 
>
> Note the difference between *names* and *full names* (cf. 
> http://aroma-project.org/definitions/namesAndTags).  In your case the 
> *names* are: 
>
> > getNames(dsC_EC500K_Sty) 
> [1] "E1507T_STY"  "E1510T_STY"  "E1520T_STY" ... "SHE1796_STY" 
> > getNames(dsC_EC500K_Nsp) 
> [1] "E1507T_Nsp"  "E1510T_Nsp  "E1520T_Nsp" ... "SHE1796_NSP" 
>
> Because of this, doCBS() fails to pair them up.  So, yes, if they would 
> be: 
>
> > getNames(dsC_EC500K_Sty) 
> [1] "E1507T"  "E1510T"  "E1520T" ... "SHE1796" 
> > getNames(dsC_EC500K_Nsp) 
> [1] "E1507T"  "E1510T  "E1520T" ... "SHE1796" 
>
> it would work as you expect.   The *names* comes directly from the 
> *full names*, which by default comes from the *file names* (see above 
> link)  Now, you don't have to rename the files to change the full 
> names.  Instead you can use so called fullname translator function, 
> which will allow you to rename *full names* "on the fly", cf. 
> http://aroma-project.org/howtos/setFullNamesTranslator.   In your case 
> you'll only have to replace the underscores (_) with a comma (,) and 
> everything will work.  So, do: 
>
> fnt <- function(names, ...) gsub("_", ",", names, fixed=TRUE); 
> setFullNamesTranslator(dsC_EC500K_Sty, fnt); 
> setFullNamesTranslator(dsC_EC500K_Nsp, fnt); 
>
> and you should get: 
>
> > getFullNames(dsC_EC500K_Sty) 
> [1] "E1507T,STY,total" "E1510T,STY,total" ... "SHE1796,STY,total" 
> > getFullNames(dsC_EC500K_Nsp) 
> [1] "E1507T,Nsp,total" "E1510T,Nsp,total" ... "SHE1796,NSP,total" 
>
> and therefore: 
>
> > getNames(dsC_EC500K_Sty) 
> [1] "E1507T" "E1510T" ... "SHE1796" 
> > getNames(dsC_EC500K_Nsp) 
> [1] "E1507T" "E1510T" ... "SHE1796" 
>
> Then retry with doCBS(). 
>
> If your GenomeWideSNP_5 arrays have completely different name formats, 
> you have to create a more fancy full names translator function that 
> takes the input names and translates them to match the above. 
>
> Hope this helps 
>
> Henrik 
>
> > 
> > 
> > On Wednesday, June 5, 2013 5:12:56 PM UTC-4, Wei Tang wrote: 
> >> 
> >> here you are 
> >> 
> >> > print(getFullNames(dsC_EC500K_Sty)) 
> >>  [1] "E1507T_STY,total"  "E1510T_STY,total"  "E1520T_STY,total" 
> >>  [4] "E1521T_STY,total"  "E1532T_STY,total"  "E1535T_STY,total" 
> >>  [7] "E1542T_STY,total"  "E1546T_STY,total"  "E1558T_STY,total" 
> >> [10] "E1566T_STY,total"  "E1572T_STY,total"  "E1573T_STY,total" 
> >> [13] "E1575T_STY,total"  "E1584T_STY,total"  "E1589T_STY,total" 
> >> [16] "E1610T_STY,total"  "E1635T_STY,total"  "E1756T_STY,total" 
> >> [19] "E1782T_STY,total"  "E1796T_STY,total"  "SHE1507_STY,total" 
> >> [22] "SHE1510_STY,total" "SHE1520_STY,total" "SHE1521_STY,total" 
> >> [25] "SHE1532_STY,total" "SHE1535_STY,total" "SHE1542_STY,total" 
> >> [28] "SHE1546_STY,total" "SHE1558_STY,total" "SHE1566_STY,total" 
> >> [31] "SHE1572_STY,total" "SHE1573_STY,total" "SHE1575_STY,total" 
> >> [34] "SHE1584_STY,total" "SHE1589_STY,total" "SHE1610_STY,total" 
> >> [37] "SHE1635_STY,total" "SHE1756_STY,total" "SHE1782_STY,total" 
> >> [40] "SHE1796_STY,total" 
> >> > print(getFullNames(dsC_EC500K_Nsp)) 
> >>  [1] "E1507T_Nsp,total"  "E1510T_Nsp,total"  "E1520T_Nsp,total" 
> >>  [4] "E1521T_Nsp,total"  "E1532T_Nsp,total"  "E1535T_Nsp,total" 
> >>  [7] "E1542T_Nsp,total"  "E1546T_Nsp,total"  "E1558T_Nsp,total" 
> >> [10] "E1566T_Nsp,total"  "E1572T_Nsp,total"  "E1573T_Nsp,total" 
> >> [13] "E1575T_Nsp,total"  "E1584T_Nsp,total"  "E1589T_Nsp,total" 
> >> [16] "E1610T_Nsp,total"  "E1635T_Nsp,total"  "E1756T_Nsp,total" 
> >> [19] "E1782T_Nsp,total"  "E1796T_Nsp,total"  "SHE1507_NSP,total" 
> >> [22] "SHE1510_NSP,total" "SHE1520_NSP,total" "SHE1521_NSP,total" 
> >> [25] "SHE1532_NSP,total" "SHE1535_NSP,total" "SHE1542_NSP,total" 
> >> [28] "SHE1546_NSP,total" "SHE1558_NSP,total" "SHE1566_NSP,total" 
> >> [31] "SHE1572_NSP,total" "SHE1573_NSP,total" "SHE1575_NSP,total" 
> >> [34] "SHE1584_NSP,total" "SHE1589_NSP,total" "SHE1610_NSP,total" 
> >> [37] "SHE1635_NSP,total" "SHE1756_NSP,total" "SHE1782_NSP,total" 
> >> [40] "SHE1796_NSP,total" 
> >> 
> >> 
> >> On Wednesday, June 5, 2013 5:01:19 PM UTC-4, Henrik Bengtsson wrote: 
> >>> 
> >>> On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang <tangw...@gmail.com> wrote: 
> >>> > Thank you, please see the info below. 
> >>> > 
> >>> > script 
> >>> > 
> >>> > dataSet_500K="EC500K" 
> >>> > 
> >>> > 
> dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType="Mapping250K_Sty",verbose=verbose)
>  
>
> >>> > 
> >>> > 
> dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType="Mapping250K_Nsp",verbose=verbose)
>  
>
> >>> > 
> >>> > dataSet="EC500K" 
> >>> > tags <- "ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY" ## OR## tags <- 
> >>> > "ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY" 
> >>> > res <- doCBS(dataSet, tags=tags, chipTypes=c("Mapping250K_Nsp", 
> >>> > "Mapping250K_Sty"), verbose=-10) 
> >>> 
> >>> Would you mind sharing the output of (all) the verbose output from the 
> >>> doCBS() call?  That would help troubleshooting (I have a guess what's 
> >>> going on).  It would also be useful to see the output of 
> >>> 
> >>> print(getFullNames(dsC_EC500K_Sty)) 
> >>> print(getFullNames(dsC_EC500K_Nsp)) 
> >>> 
> >>> If you don't want to share this on the mailing list, you can send it 
> >>> to me offline. 
> >>> 
> >>> /Henrik 
> >>> 
> >>> > 
> >>> > 
> >>> > 
> >>> >> traceback() 
> >>> > 43: file(pathname, open = "rb") 
> >>> > 42: readRawFooter.AromaTabularBinaryFile(this) 
> >>> > 41: readRawFooter(this) 
> >>> > 40: readFooter.AromaTabularBinaryFile(this) 
> >>> > 39: readFooter(this) 
> >>> > 38: getChipType.AromaUnitSignalBinaryFile(getOneFile(this), ...) 
> >>> > 37: getChipType(getOneFile(this), ...) 
> >>> > 36: getChipType.AromaUnitSignalBinarySet(X[[1L]], ...) 
> >>> > 35: FUN(X[[1L]], ...) 
> >>> > 34: lapply(X = X, FUN = FUN, ...) 
> >>> > 33: sapply(res, FUN = getChipType) 
> >>> > 32: getSets.AromaMicroarrayDataSetTuple(this) 
> >>> > 31: getSets(this) 
> >>> > 30: getNames.GenericDataFileSetList(this, ...) 
> >>> > 29: getNames(this, ...) 
> >>> > 28: length.GenericDataFileSetList(refTuple) 
> >>> > 27: length(refTuple) 
> >>> > 26: isPaired.CopyNumberChromosomalModel(this) 
> >>> > 25: isPaired(this) 
> >>> > 24: getAsteriskTags.CopyNumberSegmentationModel(this) 
> >>> > 23: getAsteriskTags(this) 
> >>> > 22: paste(getAsteriskTags(this)[-1], collapse = ",") 
> >>> > 21: getTags.CopyNumberSegmentationModel(this) 
> >>> > 20: getTags(this) 
> >>> > 19: paste(getTags(this), collapse = ",") 
> >>> > 18: paste("Tags:", paste(getTags(this), collapse = ",")) 
> >>> > 17: as.character.CopyNumberChromosomalModel(x) 
> >>> > 16: as.character(x) 
> >>> > 15: print(as.character(x)) 
> >>> > 14: print.Object(...) 
> >>> > 13: print(...) 
> >>> > 12: eval(expr, envir, enclos) 
> >>> > 11: eval(expr, pf) 
> >>> > 10: withVisible(eval(expr, pf)) 
> >>> > 9: evalVis(expr) 
> >>> > 8: capture.Verbose(this, print(...), level = level) 
> >>> > 7: capture(this, print(...), level = level) 
> >>> > 6: print.Verbose(verbose, cbs) 
> >>> > 5: print(verbose, cbs) 
> >>> > 4: doCBS.CopyNumberDataSetTuple(dsTuple, arrays = arrays, ..., 
> verbose 
> >>> > = 
> >>> > verbose) 
> >>> > 3: doCBS(dsTuple, arrays = arrays, ..., verbose = verbose) 
> >>> > 2: doCBS.default(dataSet, tags = tags, chipTypes = 
> c("Mapping250K_Nsp", 
> >>> >        "Mapping250K_Sty"), verbose = -10) 
> >>> > 1: doCBS(dataSet, tags = tags, chipTypes = c("Mapping250K_Nsp", 
> >>> >        "Mapping250K_Sty"), verbose = -10) 
> >>> > 
> >>> > 
> >>> > 
> >>> > 
> >>> >> sessionInfo() 
> >>> > R version 3.0.0 (2013-04-03) 
> >>> > Platform: x86_64-unknown-linux-gnu (64-bit) 
> >>> > 
> >>> > locale: 
> >>> > [1] C 
> >>> > 
> >>> > attached base packages: 
> >>> > [1] stats     graphics  grDevices utils     datasets  methods   base 
> >>> > 
> >>> > other attached packages: 
> >>> >  [1] R.cache_0.6.5          aroma.cn_1.3.3         DNAcopy_1.34.0 
> >>> >  [4] aroma.affymetrix_2.9.4 affxparser_1.32.1      aroma.apd_0.2.3 
> >>> >  [7] R.huge_0.4.1           aroma.light_1.30.2     aroma.core_2.9.5 
> >>> > [10] matrixStats_0.8.1      R.rsp_0.9.6            R.devices_2.2.2 
> >>> > [13] R.filesets_2.0.1       R.utils_1.23.2         R.oo_1.13.6 
> >>> > [16] R.methodsS3_1.4.2 
> >>> > 
> >>> > loaded via a namespace (and not attached): 
> >>> > [1] PSCBS_0.34.8 digest_0.6.3 tools_3.0.0 
> >>> > 
> >>> > 
> >>> > 
> >>> > On Wednesday, June 5, 2013 3:50:41 PM UTC-4, Henrik Bengtsson wrote: 
> >>> >> 
> >>> >> Hi. 
> >>> >> 
> >>> >> On Wed, Jun 5, 2013 at 11:31 AM, Wei Tang <tangw...@gmail.com> 
> wrote: 
> >>> >> > Hi Henrik , 
> >>> >> > 
> >>> >> > Thank you for you suggestion. 
> >>> >> > 
> >>> >> > but when I ran 
> >>> >> > 
> >>> >> > res <- doCBS(dataSet, tags=tags, chipTypes=c("Mapping250K_Nsp", 
> >>> >> > "Mapping250K_Sty"), verbose=verbose); 
> >>> >> > 
> >>> >> > it complained 
> >>> >> > " 
> >>> >> > Error in file(pathname, open = "rb") : invalid 'description' 
> >>> >> > argument 
> >>> >> > " 
> >>> >> > 
> >>> >> > do you know how to fix it? 
> >>> >> 
> >>> >> 1. What does traceback() output immediately after you get that 
> error? 
> >>> >> 2. Can you show me your complete script? 
> >>> >> 3. What is your sessionInfo()? 
> >>> >> 
> >>> >> > 
> >>> >> > my situation is all paired tumor-normal, 36 paired-samples in 
> SNP5 
> >>> >> > and 
> >>> >> > additional 20 paried-samples in 500K 
> >>> >> > 
> >>> >> > should I use "Multi-source copy-number normalization" 
> >>> >> 
> >>> >> Possibly - depending on the amount of attenuation in the different 
> >>> >> chip type hybridizations (depends on date, lab etc) you may see a 
> >>> >> small improvement in power to detect change points.  However, even 
> >>> >> without doing MSCN it is still always better to merge platforms (as 
> >>> >> doCBS() does) than running only single chips, cf. Figure 6 in H. 
> >>> >> Bengtsson, A. Ray, P. Spellman & T.P. Speed, A single-sample method 
> >>> >> for normalizing and combining full-resolution copy numbers from 
> >>> >> multiple platforms, labs and analysis methods, Bioinformatics 2009 
> >>> >> [http://aroma-project.org/publications]. 
> >>> >> 
> >>> >> > and how about using "doASCRMAv2", does the usage the same as 
> >>> >> > "doCRMAv2" 
> >>> >> > ?; 
> >>> >> 
> >>> >> That's if you plan to infer parent-specific CNs.  If you don't know 
> >>> >> yet, use doASCRMAv2().  Everything should work the same with 
> doCBS(). 
> >>> >> 
> >>> >> /Henrik 
> >>> >> 
> >>> >> > 
> >>> >> > Many thanks, 
> >>> >> > 
> >>> >> > Wei 
> >>> >> > 
> >>> >> > 
> >>> >> > On Thursday, May 30, 2013 6:05:55 PM UTC-4, Henrik Bengtsson 
> wrote: 
> >>> >> >> 
> >>> >> >> Hi, 
> >>> >> >> 
> >>> >> >> I've done some updates to the help pages (e.g. ?doCBS), so 
> before 
> >>> >> >> anything I recommend to update to aroma.core 2.9.5 and 
> >>> >> >> aroma.affymetrix 2.9.4: 
> >>> >> >> 
> >>> >> >> source("http://aroma-project.org/hbLite.R";); 
> >>> >> >> hbInstall("aroma.affymetrix"); 
> >>> >> >> 
> >>> >> >> 
> >>> >> >> On Tue, May 28, 2013 at 9:37 AM, Wei Tang <tangw...@gmail.com> 
> >>> >> >> wrote: 
> >>> >> >> > Hi aroma.affymetrix developers, 
> >>> >> >> > 
> >>> >> >> > Before I start the analysis, I just want to confirm the CN 
> >>> >> >> > analysis 
> >>> >> >> > of 
> >>> >> >> > 500K 
> >>> >> >> > arrays with doCRMAv2, as I did not find a Vig specific about 
> it. 
> >>> >> >> > 
> >>> >> >> > What I understand is, 
> >>> >> >> > 
> >>> >> >> > 1. run 250K_Nsp 
> >>> >> >> > dsC_Nsp=doCRMAv2(test,cdf="Nsp",verbose=verbose) 
> >>> >> >> > 
> >>> >> >> > 2. run 250_Sty 
> >>> >> >> > 
> >>> >> >> > dsC_Sty=doCRMAv2(test,cdf="Sty",verbose=verbose) 
> >>> >> >> 
> >>> >> >> Yes, you can do CRMAv2 preprocessing for each chip type 
> >>> >> >> independently. 
> >>> >> >>  However, for doCRMAv2() you need to do something like: 
> >>> >> >> 
> >>> >> >> dsC_Nsp <- doCRMAv2(dataSet, chipType="Mapping250K_Nsp", 
> >>> >> >> verbose=verbose) 
> >>> >> >> dsC_Sty <- doCRMAv2(dataSet, chipType="Mapping250K_Sty", 
> >>> >> >> verbose=verbose) 
> >>> >> >> 
> >>> >> >> Chip types have formal and strict names, cf. 
> >>> >> >> http://aroma-project.org/definitions/chipTypesAndCDFs 
> >>> >> >> 
> >>> >> >> > 
> >>> >> >> > 3. merge them together by "aroma.cn" 
> >>> >> >> 
> >>> >> >> Actually, despite its name, you don't need to aroma.cn package 
> >>> >> >> here. 
> >>> >> >> The basic CBS methods are still in the aroma.core package.  So, 
> >>> >> >> after 
> >>> >> >> doing the above doCRMAv2() processing, you then want to do 
> >>> >> >> something 
> >>> >> >> like: 
> >>> >> >> 
> >>> >> >> tags <- "ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY";  # Tags added by 
> CRMAv2 
> >>> >> >> res <- doCBS(dataSet, tags=tags, chipTypes=c("Mapping250K_Nsp", 
> >>> >> >> "Mapping250K_Sty"), verbose=verbose); 
> >>> >> >> 
> >>> >> >> It's important that the array *names* of the Mapping250K_Nsp and 
> >>> >> >> Mapping250K_Sty pair up, because that is how doCBS() know which 
> >>> >> >> array 
> >>> >> >> files to pair up/merge in the segmentation.   doCBS() match 
> array 
> >>> >> >> names using the names from getNames(), e.g. 
> >>> >> >> 
> >>> >> >> names_Nsp <- getNames(dsC_Nsp); 
> >>> >> >> names_Sty <- getNames(dsC_Sty); 
> >>> >> >> 
> >>> >> >> If they don't match up, there are way to "change" the names so 
> they 
> >>> >> >> do, cf. http://aroma-project.org/howtos/setFullNamesTranslator 
> >>> >> >> 
> >>> >> >> > 
> >>> >> >> > Would you mind telling me if I am correct with analysis? 
> >>> >> >> > 
> >>> >> >> > I also have SNP5.0 to merge, so should I merge 3 arrays at one 
> >>> >> >> > time 
> >>> >> >> > or, 
> >>> >> >> > merge 500K first and then SNP5.0? 
> >>> >> >> 
> >>> >> >> You can just include them as a third chiptype set above, e.g. 
> >>> >> >> 
> >>> >> >> res <- doCBS(dataSet, tags=tags, chipTypes=c("Mapping250K_Nsp", 
> >>> >> >> "Mapping250K_Sty", "GenomeWideSNP_5"), verbose=verbose); 
> >>> >> >> 
> >>> >> >> Hope this helps/get you started 
> >>> >> >> 
> >>> >> >> /Henrik 
> >>> >> >> 
> >>> >> >> > 
> >>> >> >> > Thank you very much, 
> >>> >> >> > 
> >>> >> >> > Wei 
> >>> >> >> > 
> >>> >> >> > NCI/NIH 
> >>> >> >> > 
> >>> >> >> > 
> >>> >> >> > 
> >>> >> >> > -- 
> >>> >> >> > -- 
> >>> >> >> > 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-af...@googlegroups.com 
> >>> >> >> > To unsubscribe and other options, go to 
> >>> >> >> > http://www.aroma-project.org/forum/ 
> >>> >> >> > 
> >>> >> >> > --- 
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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. 
> >>> >> > 
> >>> >> > 
> >>> >> > You received this message because you are subscribed to the 
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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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>
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> >>> > 
> > 
> > -- 
> > -- 
> > When reporting problems on aroma.affymetrix, make sure 1) to run the 
> latest 
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> > traceback(), and 3) to post a complete code example. 
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>

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