User: lkianmehr

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lkianmehr0
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Posts by lkianmehr

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Comment: C: How to filter tximport output for edgeR?
... Hello, excuse me, I am a bit new in R. I have used this command y$offset <- t(t(log(normMat)) + o) to make a box plot. what should be written as vertical axis title and horizontal axis title of box plot? may I also make a heatmap clustering for that? thanks in advance ...
written 4 months ago by lkianmehr0
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Comment: C: what should I do with many zero counts from Salmon quantification
... Excuse me, I would appreciate if help me to making a heatmap of the count matrix which I performed according to DESeq2 vignette, select <- order(rowMeans(counts(ddstxi,normalized=TRUE)), decreasing=TRUE)[1:20] df <- as.data.frame(colData(ddstxi)[,c("group")]) pheatmap(assay(ntd)[select,], ...
written 4 months ago by lkianmehr0
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Comment: C: what should I do with many zero counts from Salmon quantification
... exactly, it works. thanks alot ...
written 4 months ago by lkianmehr0
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Comment: C: what should I do with many zero counts from Salmon quantification
... yes, it's a DESeqDataSet. but it doesn't work! ...
written 4 months ago by lkianmehr0
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Comment: C: what should I do with many zero counts from Salmon quantification
... Excuse me, to make plotMA with res following DESeq2 vignette, it makes a plot based on expression log ratio and log expression, not LFC and mean of normalized counts, plotMA(ddsTxi, alpha= 0.1, main = "", xlab = "mean of normalized counts", ylim, mle = TRUE) I face with an error: Error in as.vector ...
written 4 months ago by lkianmehr0
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Comment: C: what should I do with many zero counts from Salmon quantification
... Sorry, I think, I made a mistake cause I've calculated log2(1+counts), and made a box plot. it's y axis is between 0 to 20. what does it mean? ...
written 4 months ago by lkianmehr0
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what should I do with many zero counts from Salmon quantification
... I have quantified the RNA-seq samples by Salmon. 2 groups are wild-type and 4 groups are Dnmt2 knocked-out. I've put all in one dataset for DE analysis. box plot of their normalized counts shows the median of knocked-out samples are zero, and maximum of 20 reads are assigned to each transcript. now ...
normalization deseq2 R salmon written 4 months ago by lkianmehr0 • updated 4 months ago by Michael Love24k
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different observation of DEG for same group
... Hello, I have 12 samples from 2 different experiment. include D1,D3 (group D); R1,R3 (group R), Dnmt2_ND1, Dnmt2_ND2 (Dnmt2_ND group), Dnmt2_NF1, Dnmt2_NF2 (Dnmt2_NF), Dnmt2_HD1, Dnmt2_HD2 (Dnmt2_HD group), Dnmt2_HF1, Dnmt2_HF2 (Dnmt2_HF group). D and R groups are wild-type mice and Dnmt2 groups ar ...
deseq2 de written 4 months ago by lkianmehr0 • updated 4 months ago by Michael Love24k
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quantifying piRNA and tRNA by Salmon
... Hello,   I have quantified piRNA and tRNA of RNA-seq by Salmon on fasta file, now to do DGE analysis may I use numreads ? what should I do because it is impossible to import them in tximport     thanks in advance ...
dge salmon written 7 months ago by lkianmehr0
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How tximport summerize transcript-level abundance to gene-level
... Hello, Excuse me, I have encounterd with one question about tximport. I have used tximport to import trancript-level abundance from Salmon to gene-level. now I want to choose some of significant genes for confirmation by RT-PCR. but I am not sure may I choose the gene or it's transcript. because ea ...
tximport written 7 months ago by lkianmehr0 • updated 7 months ago by Michael Love24k

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