User: BM

gravatar for BM
BM40
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
1 month, 3 weeks ago
Joined:
3 years, 12 months ago
Email:
b******@ucl.ac.uk

Posts by BM

<prev • 16 results • page 1 of 2 • next >
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Comment: C: DEXseq Error - SummarizedExperiment
... I tried what you suggested using option 1,now I have the following error: converting counts to integer mode Error in DESeqDataSet(rse, design, ignoreRank = TRUE) : all samples have 0 counts for all genes. check the counting script. ...
written 8 weeks ago by BM40
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DEXseq Error - SummarizedExperiment
... I have an error when performing a DEXseq count for exon usuage from RNA-seq data. DEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon ) I receive the error: Error in DEXSeqDataSetFromSE(SE, design = ~sample + exon + condition:exon) : make sure your SummarizedExperime ...
dexseq deseq2 rna-seq summarizedexperiment written 9 weeks ago by BM40 • updated 8 weeks ago by benformatics920
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Comment: A: Directional Strand related settings for RNA-seq Analysis Software
... Yes it is Smartseq v4 Ultra low input kit ...
written 3 months ago by BM40
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Directional Strand related settings for RNA-seq Analysis Software
... A question about the library preparation for RNA-seq and Directional Strand related settings for RNA-seq Analysis Software The library was prepared was using Clontech Smartseq v4 and Nextera XT So is the library directional and first strand specific (F2R1) or second strand (F1R2)? Which libray type ...
htseq tophat rna-seq smartseq hisat2 written 3 months ago by BM40 • updated 3 months ago by Juke-342.2k
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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 23 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 2.2 years ago by BM40 • updated 8 weeks ago by ATpoint19k
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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 2.4 years ago by BM40 • updated 2.4 years ago by WouterDeCoster40k
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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 2.4 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 2.4 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 3.9 years ago by BM40

Latest awards to BM

Popular Question 2.0 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 2.0 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 2.0 years ago, created a question with more than 1,000 views. For WGCNA error: Co-expression similarity and adjacency in Network Creation
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 3.6 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Deseq2 gene name annotation

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