User: mannoulag1

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mannoulag110
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Posts by mannoulag1

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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 21 days ago by mannoulag110
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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 21 days ago by mannoulag110
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Comment: C: Analysis of GEO2R
... Hi Kevin and Happy new year 2018 , Thank you for your answer , ok, for the normalisation I already did it with the function rma in my R code, this give the same result? and also I tested the gcrma normalisation with the function gcrma, what is the best method for normalisation? for defining groups ...
written 21 days ago by mannoulag110
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Analysis of GEO2R
... Hi, Can I continue the analysis after obtening the toptable of differentially expressed genes using the R code of GEO2R or I should do my own analysis? I have many samples in my dataset, how can I define the groups in GEO2R because it influence the result of the toptable. The normalization in GEO2R ...
gene R geo2r written 28 days ago by mannoulag110 • updated 25 days ago by Kevin Blighe11k
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Comment: C: extracting submatrix from microarray
... Hi Kevin, yes , thank you very much ...
written 3 months ago by mannoulag110
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Comment: C: extracting submatrix from microarray
... thank you very much, with the following code I get a submatrix but with probe-ID, this can seem true? geneList<- biomaRt::getBM(attributes = c( "ensembl_gene_id", "go_id", "affy_ath1_121501"), filters = "go", values = "GO:.....", mart = mart) subMatrix<- MyExpressionMatrix[which(rown ...
written 3 months ago by mannoulag110
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Comment: C: extracting submatrix from microarray
... ok, my matrix is large, I poste here only 10 lignes (genes) and 4 conditions: 244901_at 3.823607 4.442251 4.284493 3.709218 244902_at 4.263668 4.519978 4.465266 4.434114 244903_at 9.989272 10.102369 ...
written 3 months ago by mannoulag110
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Comment: C: extracting submatrix from microarray
... Hi, thank you. but how to subset genes of interest? my idea is to extract the genes list according to the GO term. ...
written 3 months ago by mannoulag110
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Comment: C: extracting submatrix from microarray
... Hi Kevin, Thank you very much, my expression matrix has 'array element names' (....._at) as row names, how to convert it to ensembl gene id? any idea please? ...
written 3 months ago by mannoulag110
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extracting submatrix from microarray
... I have a gene expression matrix , I would like to extract a submatrix of genes annotated by a GO term. I use the R code to have a list of genes annotated by this term: mart <- biomaRt::useMart(biomart = "plants_mart", dataset = "athaliana_eg_gene", host = 'plants.ensembl.org') GTOG ...
gene R thaliana go microarrays written 3 months ago by mannoulag110 • updated 3 months ago by Kevin Blighe11k

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