User: BM

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BM40
Reputation:
40
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New User
Location:
United Kingdom
Last seen:
1 year, 8 months ago
Joined:
3 years, 8 months ago
Email:
b******@ucl.ac.uk

Posts by BM

<prev • 12 results • page 1 of 2 • next >
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Answer: A: WGCNA error: Co-expression similarity and adjacency in Network Creation
... The count data can be transformed in DESeq2 using the variance-stabilizing transformation. The WGCNA FAQ section explains this: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html ...
written 19 months ago by BM40
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HtSeq installation error
... I have a problems installing HTSeq on windows 7. I have installed Python 2.7 and numpy, but when I input the command "setup.py install" in the comand prompt I get the error: **symlinking folders for python2 Traceback (most recent call last): File "setup.py", line 20, in os.symlink(py_fdn+fdn.fdn) ...
htseq dexseq rna-seq written 23 months ago by BM40
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DeSeq2 rlog or varianceStabilizingTransformation using ouput file
... I have a DeSeq2 output file generated by an external RNA-seq. So the output is the usual has the usual columns: gene identifiers, baseMean, log2FoldChange, lfcSE stat, pvalue, padj. However, I want to perform rlog or varianceStabilizingTransformation on my data. Is there a way to do this transformat ...
rlog vsd deseq2 rna-seq transformation written 2.1 years ago by BM40 • updated 2.1 years ago by WouterDeCoster37k
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Answer: A: WGCNA error: Co-expression similarity and adjacency in Network Creation
... Thank you all for you comments. The error was I was using raw counts, when I used transformed normalised counts, it worked. ...
written 2.1 years ago by BM40
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WGCNA error: Co-expression similarity and adjacency in Network Creation
... I have an issue with WGCNA analysis on RNA-seq data. I have an error message when calculating co-expression similarity and adjacency at the stage of network construction and module detection. So when I input the function: > adjacency = adjacency(datExpr, power = softPower) the following errror ...
wgcna network analysis rna-seq written 2.1 years ago by BM40
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Comment: C: Annotate ouput file from Deseq2
... The initial analysis was performed elsewhere. So I only have the Dexseq count file with ensemble ids of all the different exons of a gene. How can i use this file to proceed - either by annotating exons ids into a gene or using the file in Deseq2 and then annotate ? ...
written 3.5 years ago by BM40
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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 3.5 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 3.5 years ago by BM40 • updated 3.5 years ago by James Ashmore2.6k
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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 3.6 years ago by BM40 • updated 6 months ago by zx87546.8k
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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 3.7 years ago by BM40

Latest awards to BM

Popular Question 24 months ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 3.2 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Deseq2 gene name annotation

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