User: Björn

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Björn30
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Posts by Björn

<prev • 90 results • page 1 of 9 • next >
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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 1 day ago by Björn30 • updated 1 day ago by Kevin Blighe28k
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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 6 days ago by Björn30
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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 6 days ago by Björn30
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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 6 days ago by Björn30
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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 6 days ago by Björn30 • updated 6 days ago by Devon Ryan84k
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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 7 days ago by Björn30
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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 13 days ago by Björn30
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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 13 days ago by Björn30 • updated 13 days ago by zx87545.0k
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what to use in "Geneinfo" for miRNA in -TCGAanalyze_Normalization- of TCGAbiolinks
... Hi, For **mRNA** DE expression, the code used is dataNorm <- TCGAanalyze_Normalization(tabDF = dataPrep, geneInfo = geneInfo, method = "gcContent") However, what should I use for miRNAs in dataNorm <- TCGAa ...
normalization tcga mirna geneinfo written 6 weeks ago by Björn30
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(Closed) How to link non-unique colnames in two different files ?
... I have a file1 with example col names as follows *xyz-123 xyz-234 abc-345 abc-789*. Another file2 with row names *xyz abc*. How to link file2 and file1 using row names of file2. Please note *xyz-123 xyz-234* have different information from same patient. I need to link those files and process into ...
R dplyr written 7 weeks ago by Björn30

Latest awards to Björn

Popular Question 5 days ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming
Popular Question 4 weeks ago, created a question with more than 1,000 views. For How to cluster in heatmap.2
Popular Question 5 weeks ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming

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