Problem when trying to use \'affy\' package
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@kaj-chokeshaiusaha-5769
Last seen 8.1 years ago
Thank you very much, James!! I will try my best to figure this out. It's always great for naive person like me to have generous person like you in Bioconductors :) Best Regards, Kaj On Thu, Jan 30, 2014 at 9:31 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Kaj, > > If you are really interested in figuring out what the problem is, then it > will be up to you. As I already told you, I don't see anything obvious with > your script. > > Anyway, the error you see comes from stats:::simpleLoess(), which can't > have any NA values. However, this function is called by stats::loess, which > _can_ have NA values: > > y <- rnorm(1000) >> x <- rnorm(1000) >> y[sample(1:1000, 50)] <- NA >> loess(y~x) >> > Call: > loess(formula = y ~ x) > > Number of Observations: 950 > Equivalent Number of Parameters: 5.49 > Residual Standard Error: 1.061 > > But if we use stats:::simpleLoess() directly: > > stats:::simpleLoess(y,x,rep(1, 1000)) >> > Error in stats:::simpleLoess(y, x, rep(1, 1000)) : > > NA/NaN/Inf in foreign function call (arg 1) > > The reason loess() has no problems with the NA values is because it looks > at > > options("na.action") >> > $na.action > [1] "na.omit" > > and omits the paired observations where one or the other is NA. I don't > see that normalize.loess() cares much about NA values, however: > > z <- normalize.loess(cbind(x,y)) >> > Done with 1 vs 2 in iteration 1 > 1 NA > Warning message: > In normalize.loess(cbind(x, y)) : NaNs produced > > although the normalized values are really bad: > > apply(z, 2, function(x) sumis.na(x))) >> > x y > 766 766 > > So I guess the first step is to run your script and then see what you get > for options("na.action"). If that is not na.omit then you have a problem. > But if you have any NA values in your AffyBatch, you still have a problem > because you shouldn't have any. If no NA values, then you will probably > have to either debug(loess) and step through, checking for NA values being > passed in and then go back and try to find out why, or use options(error = > recover) and then inspect the various frames that come up when you hit the > error. > > Best, > > Jim > > > > > On Wednesday, January 29, 2014 9:50:36 PM, Kaj wrote: > >> On 28/01/14 00:22, James W. MacDonald wrote: >> >>> Hi Kaj, >>> >>> I don't see anything obviously wrong with your script. >>> >>> I do wonder why you are bothering with loess normalization. Maybe 10 >>> years ago, normalization of Affy arrays was a relatively hot topic, >>> but people have since pretty much settled on quantile normalization. >>> I don't mean to imply that you should be using quantile normalization >>> to normalize samples from three different experiments - that would be >>> crazy - but I don't think you will be able to do a better job with >>> cyclic loess. And none of the normalization routines are designed to >>> account for batch effects, so you shouldn't really be normalizing all >>> the arrays together anyway. >>> >>> Instead, you might consider normalizing data from each experiment >>> separately, and then using ComBat() from the sva package to remove >>> the batch effects. Alternatively you could use SCAN.UPC to summarize >>> your data. >>> >>> Best, >>> >>> Jim >>> >>> >>> On Sunday, January 26, 2014 11:42:01 PM, Kaj wrote: >>> >>>> On 22/01/14 01:24, James W. MacDonald wrote: >>>> >>>>> Hi Kaj, >>>>> >>>>> On Sunday, January 19, 2014 8:45:36 AM, Kaj Chokeshaiusaha [guest] >>>>> wrote: >>>>> >>>>>> >>>>>> Dear R helpers, >>>>>> >>>>>> I have been learning 'affy' package and currently trying 'expresso' >>>>>> function of which allows background correction, normalization, >>>>>> PMcorrection and summarization in on step. I have try 'expresso' >>>>>> with following script with the "af" Affybatch >>>>>> >>>>>> loess.none.mas <- expresso(af,normalize.method="loess", >>>>>> bgcorrect.method="none", >>>>>> pmcorrect.method="mas", >>>>>> summary.method="mas") >>>>>> >>>>>> #It continues computing till it gives an error as following >>>>>> Done with 5 vs 22 in iteration 1 >>>>>> Done with 5 vs 23 in iteration 1 >>>>>> Done with 5 vs 24 in iteration 1 >>>>>> Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, >>>>>> normalize, : >>>>>> NA/NaN/Inf in foreign function call (arg 1) >>>>>> >>>>>> Could you please tell me what happens and how to correct it? >>>>>> >>>>> >>>>> You will need to give us more information than that. How did you >>>>> generate the AffyBatch you are using? What array? What exactly are >>>>> you trying to do? >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> >>>>>> >>>>>> -- output of sessionInfo(): >>>>>> >>>>>> R version 2.15.3 (2013-03-01) >>>>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] LC_COLLATE=Thai_Thailand.874 LC_CTYPE=Thai_Thailand.874 >>>>>> [3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C >>>>>> [5] LC_TIME=Thai_Thailand.874 >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 >>>>>> [4] zlibbioc_1.4.0 >>>>>> >>>>>> -- >>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>> >>>>> -- >>>>> James W. MacDonald, M.S. >>>>> Biostatistician >>>>> University of Washington >>>>> Environmental and Occupational Health Sciences >>>>> 4225 Roosevelt Way NE, # 100 >>>>> Seattle WA 98105-6099 >>>>> >>>> Dear James, >>>> >>>> I'm tremendously sorry for my late response. >>>> >>>> Thank you very much for your attention and reply. Here attached the >>>> script I have tried lately. What I want to do is to pre-process CEL >>>> files of canine affymetrix platform acquired from different >>>> experiments. >>>> >>>> Thank you very much again for your help. >>>> >>>> Best Regards, >>>> Kaj >>>> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> >> Dear Jim, >> >> To tell you the truth, I already try other normalization methods >> combined with batch correction using ComBat. I'm trying to determine >> which methods are the best to pre-process the data. >> >> There should be something wrong with my script trying Cyclic Loess. >> Could you please guide me a bit? >> >> Best Regards, >> Kaj >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > [[alternative HTML version deleted]]
Normalization GO affy sva SCAN.UPC Normalization GO affy sva SCAN.UPC • 894 views
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