User: Björn

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Björn40
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Posts by Björn

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Comment: C: How to create design matrix for confounder (here sunlight) in edgeR ?
... Thanks for the comment. For effect of vitD with sunlight..is it `vitD_y_Sun_y - vitD_n_Sun_y` or `vitD_y_Sun_y - vitD_n_Sun_n` One more question. I created heatmap using heatmap.2 for both contrasts which gives the same heatmap. Why is it ? I created `toptags` for both contrasts separately which g ...
written 18 months ago by Björn40
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How to create design matrix for confounder (here sunlight) in edgeR ?
... The scenario is like this. A study population given "vitamin D supp" (yes/no variable) and followed up to measure outcome "skin cancer" (again yes/no). The design matrix (1) I used is design<-model.matrix(~0+vitd, data) colnames(design) [1] "vitd" "vitdn" "vitdy" The patients w ...
rnaseq edger written 18 months ago by Björn40 • updated 18 months ago by Benn7.9k
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TCGA patient variable data dictionary
... Hi, I downloaded miRNA seq and patient data from TCGA-PRAD. Is there a way to find out the explanation /dictionary on patient/clinical variable colnames(tcga-prad) [1] "bcr_patient_barcode" "additional_studies" [3] "tumor_ti ...
tcga mirna written 18 months ago by Björn40 • updated 18 months ago by Kevin Blighe56k
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Comment: C: Problem with low count removal in edgeR ?
... I believe those with counts below 1 CPM (which includes 0) will be excluded in "keep" so why it is still a problem. ...
written 18 months ago by Björn40
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Comment: C: Problem with low count removal in edgeR ?
... Is it really a problem after using keep<-rowSums(cpm>1)>=6 table(keep) ...
written 18 months ago by Björn40
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Comment: C: Problem with low count removal in edgeR ?
... My concern is why there is still zero counts (in some samples)? ...
written 18 months ago by Björn40
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Comment: C: Problem with low count removal in edgeR ?
... I followed the paper [literature][1] and after this step o<-order(qlfGrAvsGrB$table$PValue) cpm(y)[o[1:25],] produces list of miRNAs "with zero" counts. See attached file. The row numbers are ID for miRNAs. while each column represents sample. ![figure][2] [1]: https://f1000researc ...
written 18 months ago by Björn40 • updated 18 months ago by Devon Ryan94k
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Problem with low count removal in edgeR ?
... I used following command to remove zero counts using edgeR package y<-DGEList(data, genes = miRNAs_ID,group = diagnostics, remove.zeros = T) which removed nearly 1000 miRNA (rows) from subsequent "y" that is used for analysis. Following command to exclude low counts was keep<-rowSum ...
edger differential expression mirna written 18 months ago by Björn40
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Comment: C: How to color subset of row ?
... found the answer color<-c("red","darkolivegreen", "brown4","darkgoldenrod3", "deeppink2","bisque"[6:44]) color[is.na(color)]<-"bisque" ...
written 19 months ago by Björn40
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(Closed) How to color subset of row ?
... For example, I have a column x<-c(a, b, c, D, E, F, G, H,I..........X,Y,Z) How can I create a color parameter such that a = red b= green c= blue and rest of UPPERCASE into one specific color e.g. "black" ...
R written 19 months ago by Björn40 • updated 19 months ago by zx87549.1k

Latest awards to Björn

Popular Question 18 months ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming
Popular Question 18 months ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming
Popular Question 19 months ago, created a question with more than 1,000 views. For How to cluster in heatmap.2
Popular Question 19 months ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming

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