VSN exclusion of probes
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@hans-ulrich-klein-1945
Last seen 6 hours ago
United States
Dear All, I want to normalize two-color oligo-arrays with the VSN method. The arrays contain some blank spots, which have a much stronger dye bias than the oligo spots. Therefore, I do not want them to be used by the LTS for parameter estimation. However, they should be normalized after parameter estimation. I tried the following code: (RG is a RGList object holding the Raw data) RG <- backgroundCorrect(RG, method="subtract"); y <- cbind(RG$G, RG$R); subSet <- RG$genes$Status != "blank"; # exclude blank spots vsnres <- vsn(y[subSet, ], strata=RG$genes$Block[subSet]); pars <- preproc(description(vsnres))$vsnParams; y <- vsnh(y, pars, strata=RG$genes$Block); The last statement leads to this error message: Error in vsnh(y, pars, strata = RG$genes$Block) : Invalid argument 'e_y', must be a real matrix. What is wrong with my code? What is 'e_y'? Is there a convenient way to use weights (e.g. stored in RG$genes$weights) for parameter estimation? It would be nice to exclude only the k-th probe on array i and not the k-th probe of all arrays (as done above). Regards, Hans-Ulrich -- Westf?lische Wilhelms-Universit?t M?nster Department of Medical Informatics and Biomathematics Hans-Ulrich Klein, Domagkstr. 9 (Raum 27), 48149 M?nster probe vsn oligo probe vsn oligo • 442 views ADD COMMENT 0 Entering edit mode Naomi Altman ★ 6.0k @naomi-altman-380 Last seen 6 months ago United States I am starting to use GOstat, and there are several things I do not understand. I managed to get output from HyperGTest. I was able to view the enriched categories using htmlReport. I would like to try out the graphing methods, but I have not been able to figure out the input. In particular, I assume that since I have created a GOHyperGResult object, I should use getGoGraph but I have not figured out what goes into the goIds argument. I presume it is some type of node identifier, but where do I find it? Thanks for any assistance. Naomi Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111 ADD COMMENT 0 Entering edit mode Hi Naomi, Naomi Altman wrote: > I am starting to use GOstat, and there are several things I do not understand. > > I managed to get output from HyperGTest. I was able to view the > enriched categories using htmlReport. > > I would like to try out the graphing methods, but I have not been > able to figure out the input. In particular, I assume that since I > have created a GOHyperGResult object, I should use > > getGoGraph > > but I have not figured out what goes into the goIds argument. I > presume it is some type of node identifier, but where do I find it? The getGoGraph() function wants a GOHyperGParams object, rather than a GOHyperGResult object. The goIds would then be the GO IDs that you are interested in, which can be read from the table produced by htmlReport(). Anyway, I can't get getGoGraph() to ouput what I would expect. It appears to use GOXXCHILDREN to produce the graph, whereas the other functions in the examples for that (and related) function(s) use GOXXPARENTS. To get what I would expect, you can simply use GOGraph(). Say the top three GO IDs in your table are ("GO:0019219" "GO:0019222" "GO:0006350"). Then you can get a graph by: grph <- GOGraph(c("GO:0019219" "GO:0019222" "GO:0006350"), GOBPPARENTS) plot(grph) HTH, Jim > > Thanks for any assistance. > > Naomi > > > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. ADD REPLY 0 Entering edit mode An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061127/ e7c945eb/attachment.pl ADD REPLY 0 Entering edit mode @wolfgang-huber-3550 Last seen 11 weeks ago EMBL European Molecular Biology Laborat… Dear Hans-Ulrich, thanks for your good questions! Answers see below. > I want to normalize two-color oligo-arrays with the VSN method. The > arrays contain some blank spots, which have a much stronger dye bias > than the oligo spots. Therefore, I do not want them to be used by the > LTS for parameter estimation. However, they should be normalized after > parameter estimation. > > I tried the following code: > (RG is a RGList object holding the Raw data) > > RG <- backgroundCorrect(RG, method="subtract"); > y <- cbind(RG$G, RG$R); > subSet <- RG$genes$Status != "blank"; # exclude blank spots > vsnres <- vsn(y[subSet, ], strata=RG$genes$Block[subSet]); > pars <- preproc(description(vsnres))$vsnParams; > y <- vsnh(y, pars, strata=RG$genes$Block); > > > The last statement leads to this error message: > Error in vsnh(y, pars, strata = RG$genes$Block) : > Invalid argument 'e_y', must be a real matrix. > > > What is wrong with my code? What is 'e_y'? Try y <- vsnh(y+0, pars, strata=RG$genes$Block) this should work. The (arcane) reason for this is that (I suppose) your matrix "y" is of storage mode "integer", while the C code in vsn expects type double. This is not really sth the user should be concerned with, and I plan to make a big and shiny revision of "vsn" over the Christmas holidays that will avoid this problem, and also allow to use missign values or weights as you suggest below (which you cannot presently do). > Is there a convenient way to use weights (e.g. stored in > RG$genes$weights) for parameter estimation? It would be nice to exclude > only the k-th probe on array i and not the k-th probe of all arrays (as > done above). Best wishes Wolfgang -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber