User: mannoulag1

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mannoulag120
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1 year, 6 months ago
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Posts by mannoulag1

<prev • 24 results • page 1 of 3 • next >
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Comment: C: EnhancedVolcano with gene names
... perfect !!! Thank you kevin ...
written 11 days ago by mannoulag120
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Comment: C: EnhancedVolcano with gene names
... how can I use this in lab attribute? thank you ...
written 11 days ago by mannoulag120
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Comment: C: EnhancedVolcano with gene names
... Hi Kevin, yes thank you very much for providing EnhancedVolcano, I am very interested to use it :) I succeeded to obtain the gene symbols from biomart, so I have ensemble_gene_id and the symbols but how can I use this in lab attribute? thank you ...
written 11 days ago by mannoulag120
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EnhancedVolcano with gene names
... Hi, I used EnhancedVolcano to obtain a nice volcano plot but I need the gene names in the figure not the gene ID, tt is the result of toptable, Thank you tt<-topTable(fit2, adjust="fdr", number=Inf) EnhancedVolcano(tt,lab = rownames(tt),x = "logFC", y = "adj.P.Val",pCutoff = 0.05,FC ...
R enhancedvolcano limma written 11 days ago by mannoulag120
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Comment: C: filtering genes by pearson correlation
... Thank you Jean-karim ...
written 6 months ago by mannoulag120
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Comment: C: filtering genes by pearson correlation
... Thank you Jean-Karim, I do this : #cor is symmetric, so we can keep only the half of the pairs of indices idx<-which( (abs(cor) > 0.8) & (upper.tri(cor)), arr.ind=TRUE) correlated.genes <- matrix[idx, ] Then I have to remove the duplicated genes from 'correlated.genes' ? ...
written 6 months ago by mannoulag120
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filtering genes by pearson correlation
... Hi biostars, I did a pearson correlation to my data (expression matrix), and I keep only the correlation >0.8 . How can I obtain the sub expression matrix of only these highly correlated genes. Thank you data<-t(matrix) cor = cor(data, use="pairwise.complete.obs", method="pearson") ...
cor() R rna-seq written 6 months ago by mannoulag120 • updated 6 months ago by Jean-Karim Heriche16k
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isa biclustering algorithm
... Hi, I need to do the isa biclustering algorithm on gene expression data matrix using ISA function of the Package ‘eisa’ library(eisa) thr.gene <- 2.7 thr.cond <- 1.4 set.seed(1) # to get the same results, always modules<- ISA(matrix, thr.gene=thr.gene, thr.cond= ...
R biclustering isa eisa gene expression data written 7 months ago by mannoulag120
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Comment: C: How filter genes to construct co-expression network?
... you can use the following code to filter 50% of genes: Library(genefilter) genes<-varFilter(exp) or this code for example to keep only 20%of genes: genes<-varFilter(exp, var.func=IQR, var.cutoff=0.8, filterByQuantile=TRUE) ...
written 9 months ago by mannoulag120
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Comment: C: Analysis of GEO2R
... thank you, I am analysing this dataset from the Affymetrix ATH1 microarray: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5632 ...
written 9 months ago by mannoulag120

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