User: rna seq

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rna seq90
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Posts by rna seq

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Comment: C: How do use disperions estimated from my within group estimates to calculate diff
... WIll the following setup estimate within group variances for the control and treatment?  library(DESeq2) c_frame<-read.csv("data.csv", header=T, sep=",", row.names=1) condition <- factor(c(rep("control", 4), rep("treatment", 4))) coldata <- data.frame(row.names=colnames(c_frame), condit ...
written 3.2 years ago by rna seq90
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Comment: C: How do use disperions estimated from my within group estimates to calculate diff
... Let us say I have 8 samples. The first 4 are control and the second 4 are treatment. b_frame<-read.csv("input_data.txt", header=T,  row.names=1) #b_frame<-na.omit(b_frame) condition <- factor(c(rep("control", 4), rep("treatment", 4))) ##create column data coldata <- data.frame(row.names ...
written 3.2 years ago by rna seq90
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Comment: C: How do use disperions estimated from my within group estimates to calculate diff
... Hi, Here is my code: b_frame<-read.csv("input_data.txt", header=T,  row.names=1) #b_frame<-na.omit(b_frame) condition <- factor(c(rep("A", 3), rep("B", 3))) ##create column data coldata <- data.frame(row.names=colnames(b_frame), condition) ##make DESeqDataSetFromMatrix dds<-DESeqDa ...
written 3.3 years ago by rna seq90
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Answer: A: How do use disperions estimated from my within group estimates to calculate diff
... please refer to code in reply ...
written 3.3 years ago by rna seq90
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Answer: A: How do use disperions estimated from my within group estimates to calculate diff
... Hi Michael, The majority of my genes are differentially expressed between conditions. If I plot the estimated dispersion WITHIN conditions either treated or control, my dispersions are much less then when I include all samples both WITHIN and BETWEEN groups. Perhaps I am missing something here/no ...
written 3.3 years ago by rna seq90
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How do use disperions estimated from my within group estimates to calculate differential expression between groups?
... Hello, I have 8 samples. 4 control and 4 treated. I can obtain a within sample dispersion estimate if I make a dds object using only the control samples. condition <- factor(c(rep("Control1", 2), rep("Control2", 2))) And obtain dispersion estimate from this WITHIN group comparison. I would li ...
deseq2 estimatedispersions written 3.3 years ago by rna seq90
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Comment: C: problem using >3 clusters with Quasr
... Reposting new question under title: "error when genomeFile too big when running Quasr on >3 clusters" ...
written 3.8 years ago by rna seq90
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error when genomeFile too big when running Quasr on >3 clusters
... I am following up from a different post,  "problem using >3 clusters with Quasr",  as I have identified a distinct issue. Issue: When I run: library(QuasR) library(parallel) cl<-makeCluster(4) sampleFile2<-("sample_file.txt") genomeFile<-("reference_genome.fa") and reference_genome.f ...
quasr parallel cluster written 3.8 years ago by rna seq90
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Comment: C: problem using >3 clusters with Quasr
... Thanks Martin, Your code works fine. I think I have identified the problem with my code. When my genomeFile smaller ~500 sequences, the code works fine. When my genome file is > 1200 sequences, I get the error:     one node produced an error: Error on ip-172-31-10-100 processing sample /tmp/R ...
written 3.8 years ago by rna seq90
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Comment: C: problem using >3 clusters with Quasr
... The cluster call works fine clusterCall(cl, myfunc, myfunc_argument)" no error As you say, I think the problem is with QUASR library(QuasR) library(parallel) cl<-makeCluster(4) sampleFile2<-("sample_file.txt") genomeFile<-("reference_genome.fa") proj2 <- qAlign(sampleFile2, genom ...
written 3.8 years ago by rna seq90 • updated 3.8 years ago by Martin Morgan ♦♦ 24k

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