User: rhasanvandj

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rhasanvandj20
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Posts by rhasanvandj

<prev • 84 results • page 1 of 9 • next >
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(Closed) heatmap for HTSeq data in R
... Hi friends I try to plot heatmap for significant genes with cut off FDR < 0.05 and Fold change abs(2). I have two question: 1) I want to have range of my colors -3 to 3 as my minimum and maximum values are in the file. I dont know why are change it to -4 to 4. How can I set this? 2) How can I clu ...
rna-seq written 4 hours ago by rhasanvandj20
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Comment: C: row names change in normalization
... Thanks Here is my code: mat <- read.table("mydata.txt", sep = '\t', header = TRUE, row.names = 1, stringsAsFactors = FALSE, check.names=FALSE) mat1 <- as.matrix (mat) ####################normalize and log2transform mat2 <- rlog(mat1) ###### here ro ...
written 1 day ago by rhasanvandj20 • updated 1 day ago by RamRS30k
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row names change in normalization
... Hello friends I have a problem with R. I change my data file and use `rlog()` in Deseq2 to normalize and log transform my data. When I normalize my data in the resulted file the first column which is my gene names turns into numbers(1, 2, 3, 4, ....) What should I do to avoid this? I want to keep t ...
rna-seq written 1 day ago by rhasanvandj20
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Comment: C: Box plot for rna seq data
... Thanks Hamid ...
written 3 days ago by rhasanvandj20
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Comment: C: Box plot for rna seq data
... Thanks I dont know why I get error: data <- read.table ("data.txt",check.name = FALSE, row.names =1, header = T) dat <- as.data.frame(data) melt.dat <-data.frame(reshape::melt(dat, id.vars = "Gene")) Error: id variables not found in data: Gene > ...
written 4 days ago by rhasanvandj20
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Comment: C: Box plot for rna seq data
... Sorry I dont understand how the input data here is look like. I am not sure if my data format is appropriate for the code. patients in columns vs genes in rows( I know I should normalize and log2 transform). the problem is the appearance of my data and how can I have all the patients in x axis and ...
written 4 days ago by rhasanvandj20
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Comment: C: Box plot for rna seq data
... Thank you Hamid. these are really informative. I dobnot see any RNA seq expression values in this dataset you used. it is just patient names and gene list. Is there any way to plot this for significant gene expression? I want to compare expression level in patients. I want each plot to have expres ...
written 4 days ago by rhasanvandj20
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Comment: C: Box plot for rna seq data
... Hi Hamid Thanks this is for one column vs one row data. I do not know how to do it for 64 genes (rows) vs 88 patients (columns). I want patients is x axis and genes in y axis. ...
written 4 days ago by rhasanvandj20
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Box plot for rna seq data
... Hi friends I plotted this box-wisker for TCGA HTSeq data in R. I want to have harf of them as red and half as blue (control vs treatment groups). or is there any better way for boxplot? How can I do that? I just used simple code: data <- read.table("mydata.csv", header=TRUE, row.names = 1) ...
rna-seq written 4 days ago by rhasanvandj20 • updated 4 days ago by Hamid Ghaedi580
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Comment: C: heatmap in R
... yes you are right. It was just a trial. One thing that I want to do is clustering inside each of two groups. How can I do clustering for each group separately? ...
written 9 days ago by rhasanvandj20

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