User: Seymoo

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Seymoo0
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Posts by Seymoo

<prev • 28 results • page 2 of 3 • next >
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Comment: C: Probe summerization of Human HT-12 V4 BeadChip arrays
... Hi @Mark, I am using BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31) I have not manage to solve the problem yet. I manage to download the data matrix with gse <- getGEO("GSE73255", GSEMatrix = FALSE) but eset <- as(gse, "Expres ...
written 18 months ago by Seymoo0
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Comment: C: Probe summerization of Human HT-12 V4 BeadChip arrays
... Thanks for the hints Chris! I have always been working with Affy arrays so I have not much of idea about the the beadarrays. But I am gonna look into what you have suggested. ...
written 18 months ago by Seymoo0
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Probe summerization of Human HT-12 V4 BeadChip arrays
... I am not familiar with Iluumina arrays I need some hints because I am trying to work with a data set from Human HT-12 V4 BeadChip array deposited at GEO : "GSE73255" I am following to 2 approaches to get the data explaned in Beadarray package: library(GEOquery) url <- "ftp://ftp.ncbi.nih.go ...
normalization beadarray bead chip rma illuminahumanv4.db written 18 months ago by Seymoo0 • updated 18 months ago by James W. MacDonald50k
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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 18 months 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 18 months 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 18 months 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 ...
genet genetclassifier written 18 months ago by Seymoo0
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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 18 months 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 18 months ago by Seymoo0 • updated 18 months ago by Gordon Smyth37k
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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 19 months ago by Seymoo0 • updated 19 months ago by saibar20

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