User: Seymoo

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Seymoo0
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Oslo
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Posts by Seymoo

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Changing SVM-Kernal in geNetClassifier function
... Hi Dario, Thanks a lot for your answer and the the great tip about the `caret` package. The main reason I am using this package is that it outpust a list of discriminant genes for each of putative sub-classes in my data. Is that an option in the packages you mentioned above? It's very tempting wi ...
written 6 days ago by Seymoo0
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Comment: C: Normalization of multiple HTA 2.0 arays using SCAN.UPC
... Hi Stephen, I tried your suggestion, and this time R did not throw and error, but the function ran for 15 min for 20 arrays and slowed my PC entirely. RAM consumption during the function execution was above 80% ( of 24GB RAM) all the time! This process with affy::justRMA() takes less than a min on ...
written 6 days ago by Seymoo0
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Normalization of multiple HTA 2.0 arays using SCAN.UPC
... I am trying to run and compare `SCAN` function of package `SCAN.UPC` , since in the paper the authors showed superior performance to RMA method. I have a cohort of Affymetrix HTA 2.0 arrays, save on my drive. when I run the code below ` library(SCAN.UPC) library(hta20hsentrezgprobe) library(hta20 ...
scan.upc written 6 days ago by Seymoo0
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Changing SVM-Kernal in geNetClassifier function
... I am using `geNetClassifier` function of same name package to build a classifier for gene-expression data. `@classifier` slot of returned function provide information on call as below `Call: svm.default(x = t(esetFilteredDataFrame[buildGenesVector, trainSamples, drop = FALSE]), y = sampleLabels ...
svm genetclassifier written 6 days ago by Seymoo0 • updated 6 days ago by Dario Strbenac1.4k
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Comment: C: Venndigram of LIMMA decideTests() function for more than 5 sets
... Thanks for your suggestion Aaron, I will look in that. ...
written 14 days ago by Seymoo0
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Venndigram of LIMMA decideTests() function for more than 5 sets
... I'd like to make Venn diagram from Limma `decideTests` results. Limma `vennDiagram` function is limited to maximum of 5 sets. I tried to make the plot using `veneluer` and 'vennerable` packages in R but I was not successful. appreciate if someone could help me with this issue. Thanks a lot! ...
limma venn diagram vennplot written 16 days ago by Seymoo0 • updated 16 days ago by Gordon Smyth32k
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issue with FEA - Gene-Term Linker in FGNet package
... ` serverWS = "http://gtlinker.cnb.csic.es:8182" ` in fea_gtLinker() function is not responding. R throws error below ` Error in function (type, msg, asError = TRUE) : Failed to connect to gtlinker.cnb.csic.es port 8182: Timed out `   Anyone has similar problem? ...
fgnet written 27 days ago by Seymoo0 • updated 27 days ago by saibar20
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Comment: C: BioQC R package issue with broad gmt files
... Problem Solved by using `readGmt` `gmt <- Sys.glob("E:/files/Rspace/geneset.gmt")` `gmt <- readGmt(gmt)` ...
written 6 weeks ago by Seymoo0
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BioQC R package issue with broad gmt files
... I am trying to use a gmt file from broad with wmwTest instead of the gmt file included in the package, but I get `Error in FUN(X[[i]], ...) : index must be either integer vector` in R. I tried to ways of importing the gmt file as below, none were successful. `gmt <- Sys.glob("E:/files/Rspace/gen ...
R gsea gmt bioqc written 6 weeks ago by Seymoo0
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Comment: C: Retriving Annotation for HTA2.0 using biomRt
... Here are some more prob IDS Mike [1] "2824546_st" "2824549_st" "2824551_st" "2824554_st" "2827992_st" "2827995_st" "2827996_st" "2828010_st" "2828012_st" [10] "2835442_st" "2835447_st" "2835453_st" "2835456_st" "2835459_st" "2835461_st" "2839509_st" "2839511_st" "2839513_st" [19] "2839515_st" "28 ...
written 7 months ago by Seymoo0

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