User: Seymoo

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Seymoo0
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Posts by Seymoo

<prev • 31 results • page 2 of 4 • next >
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Comment: C: Multiple comparison of coefficients in limma
... Thanks a lot for explanation @Aaron Lun. ...
written 22 months ago by Seymoo0
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Comment: C: Multiple comparison of coefficients in limma
... Hi James, So because now I am comparing them against the mean, to do similar comparison would it be better to formulate it like this cm1 <- makeContrasts(G1VsG2 = G1-G2, G1VsG3 = G1-G3, G1VsG4 = G1-G4, G2VsG3 = G2-G3, ...
written 22 months ago by Seymoo0
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Multiple comparison of coefficients in limma
... In a cohort of cancer samples there are 4 groups, G1 to G4. I want to perform differential gene expression between group1 Vs all other groups, i,e, G1 = G1-(G2+G3+G4)/3, to determine DEGs for group 1. I could just find an example in limma guide where pair-wise comparisons being made ( under 9.3. se ...
limma written 22 months ago by Seymoo0 • updated 22 months ago by James W. MacDonald51k
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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 22 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 23 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 23 months ago by Seymoo0 • updated 22 months ago by James W. MacDonald51k
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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 23 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 23 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 23 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 23 months ago by Seymoo0

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