User: BM

gravatar for BM
BM40
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
6 months, 3 weeks ago
Joined:
4 years, 4 months ago
Email:
b******@ucl.ac.uk

Posts by BM

<prev • 16 results • page 2 of 2 • next >
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Comment: C: Annotate ouput file from Deseq2
... ENSMUSG00000000001:001; ENSMUSG00000000001:002 - these refer to the the different exons of the gene. So the question I suppose is how to combine or merge the different exon counts for the same gene into one count for the gene? Can this be done in Dexseq or Deseq2? ...
written 4.3 years ago by BM40
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Annotate ouput file from Deseq2
... I am trying to annotate the results output file from Desq2 so it contains gene names and symbols. The RNA-seq count file I have used comes from Dexseq and contains ensembl transcript ID: ENSMUSG00000000001:001 ENSMUSG00000000001:002 ENSMUSG00000000001:003 etc. I have tried various methods to an ...
annotate biomart deseq2 rna-seq map ids written 4.3 years ago by BM40 • updated 4.3 years ago by James Ashmore2.7k
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Deseq2 gene name annotation
... I am trying to annotate the Ensemble ID in the Deseq2 results file and add a column of Gene symbols and gene names. I have tried to use Biomart and also AnnotationDb/org.Mm.eg.db. This is the ouput library(DESeq2) # Loading required package: Rcpp # Loading required package: RcppAr ...
ensembl biomart gene symbol rna-seq deseq1 written 4.4 years ago by BM40 • updated 14 months ago by zx87548.8k
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Comment: C: RNA-seq Anova on three groups
... The data has been aligned using TopHat and counts performed using Dexseq. I am trying to use Deseq2 for differential expression, but my experience of R  is limited. 1. I am having difficulty constructing the metadata on each of the samples (columns of the count table). I can load the sample info, b ...
written 4.4 years ago by BM40
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Comment: A: RNA-seq Anova on three groups
... Thanks. But what is the formula for doing this in DESeq2. So will Deseq2 analyse all three groups at once or only two (which I thought was the case). And also if all three are analysed in ANOVA/ANODEV, are pairwise compaisions performed an p-values listed for all pairwise comparisons or an overall c ...
written 4.4 years ago by BM40
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RNA-seq Anova on three groups
... Hi, I would like some advice on RNA-seq analysis. I have three groups (control, mutant 1 and mutant 2). we would like perform a one-way anova/GLM and to analyse all three groups pair wise. So analyse all three groups to test for significance, then esablish if any gene is changed bewteenany of the g ...
anova deseq2 rna-seq edger ancodev written 4.4 years ago by BM40 • updated 4.4 years ago by Michael Love1.9k

Latest awards to BM

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 2.4 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 2.4 years ago, created a question with more than 1,000 views. For WGCNA error: Co-expression similarity and adjacency in Network Creation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 4.0 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Deseq2 gene name annotation

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