User: Biorunner88

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Biorunner8810
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Spain
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2 years, 10 months ago
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Posts by Biorunner88

<prev • 25 results • page 1 of 3 • next >
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Comment: A: Limma RNAseq comparison with Cuffdiff
... Update, I've modify the classes vector such classes <- factor(c("NEG","NEG","NEG", "MDK","MDK","MDK"), as.character(c("NEG", "MDK"))) Now logFC are quite close to the ones obtained in cuffdiff but none of the top 7 significant genes from cuffdiff are significant in limma. 3157 significant gen ...
written 12 days ago by Biorunner8810
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Limma RNAseq comparison with Cuffdiff
... I've the output of a differential expression analysis for RNA done with cuffdiff and I'm trying to check it with limma but I'm not getting the results that I would expect. w164 <- read.table("COUNTfile.txt", header = T, row.names = 1) head(w164) WM164_NEG_1 WM164_NEG_2 WM164_NEG_3 W ...
limma written 12 days ago by Biorunner8810 • updated 12 days ago by Gordon Smyth31k
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Comment: C: sampleNames differ between assayData and phenoData
... The identical() test returns a FALSE, so thats is the problem. Thanks for the answer. ...
written 15 months ago by Biorunner8810
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sampleNames differ between assayData and phenoData
... Sorry for this question, but for some reason something is happening that I'm not able to find. I'm having the next problem while creating the expression set.     pd <- data.frame(state = colnames(q@mat)) rownames(pd) <- pd[,1] pd[,1] <- 1 pheno = new("AnnotatedDataFrame" ...
expresionset written 15 months ago by Biorunner8810 • updated 15 months ago by Martin Morgan ♦♦ 20k
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Comment: C: Linear model after imputation (impute.knn function)
... ¿How it handles with missing data when for example just two points are available for a lm? And just another question. I've been discussing with a mate whether lmfit actually gives you a moderated-t statistic or not. In the vignetting it doesn't say, as it does for eBayes, but after checking, both  ...
written 2.3 years ago by Biorunner8810 • updated 2.3 years ago by Gordon Smyth31k
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Comment: C: Linear model after imputation (impute.knn function)
... Well. I understand that so, but if no k neighbor are found (because for example a gene has no data at all), the average of the column is used to fill that empty point. I do not understand why the average is also used when out of seven points; a gene has two values and five NA values. Cannot find K n ...
written 2.3 years ago by Biorunner8810
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Linear model after imputation (impute.knn function)
... Hi. I'm using this function to impute missing values in my arrays. After using it, I run a linear model for each gene, then I take t-values from each model and I plot in a boxplot. Some of the outliers in the original data (without imputation) are genes with just two data points. I expected to see ...
impute written 2.3 years ago by Biorunner8810 • updated 2.3 years ago by Gordon Smyth31k
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Comment: C: loadGSC() Piano package
... Thanks for it. I already solved it. I've another question. I'm reviewing some of what I've done and I saw that after running the function consensusHeatmap with mean, maxmean, gsea, page, median, sum and wilcoxon outputs and with the mean method I get p-values of 0 (0.0000000) or some gene sets. Is ...
written 2.3 years ago by Biorunner8810
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Mixing list from Piano package output
... Hi. I have use the piano package to create list of Gene Ontology groups ordered from top differentially expressed (up regulated groups) to down differentially expressed (down regulated groups) including all the groups between both extremes. I have used the function consensusHeatmap, so I have a co ...
piano list written 2.4 years ago by Biorunner8810 • updated 2.4 years ago by Leif Väremo60
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Comment: C: loadGSC() Piano package
... Is there any problem if there are two or more rows with the same gene and GO id in the dataframe used for the loadGSC function? Or should I delete duplicated rows?   I'm guessing this is due to the possibility that in org.Sc.sgd package the same gene has different evidences and so it appears dupli ...
written 2.5 years ago by Biorunner8810

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