User: russhh

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russhh2.7k
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UK, U. Glasgow
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@haematobot
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Bioinformatics etc of leukaemia at University of Glasgow
 

Posts by russhh

<prev • 415 results • page 1 of 42 • next >
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Comment: C: Changing the direction of logfold change?
... What do you want the logFC values to look like: do you want positive signs if there is higher expression in the treatment than the control? I wouldn't include that final line, I'd modify your line where `et` is defined: `pair = c('ctrl', 'tr')` should give the reflection of `pair = c('tr', 'ctrl')`. ...
written 10 days ago by russhh2.7k
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Comment: C: Adding gene ID in edgeR
... This is a different issue. Post a question in a separate thread. And could you please post the solution you found to your initial problem within this thread ...
written 16 days ago by russhh2.7k
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Comment: C: Adding gene ID in edgeR
... You're searching against biomarts collection of ensembl-gene ids using NCBI transcript IDs as input. Hence the NAs. ...
written 16 days ago by russhh2.7k
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Comment: C: Downloading HISAT2-2.0.1 NOT possible
... hisat2 2.0.1 beta is installable from bioconda if that's any [help][1] [1]: https://anaconda.org/bioconda/hisat2/files ...
written 16 days ago by russhh2.7k
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Comment: C: Error while running rnaseq_pipeline.sh provided by hisat2
... If the example file doesn't exist, obtain it from the hisat2 website, then try running it again. I don't see why the shell script should be considered to be faulty yet: please check that ./hisat2/chrX\_data/samples exists (relative to your current working directory) and that ERR188044_chrX.alnstats ...
written 5 weeks ago by russhh2.7k
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Comment: C: Error while running rnaseq_pipeline.sh provided by hisat2
... Does the file exist? ...
written 5 weeks ago by russhh2.7k
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Comment: C: bash script for RNA seq analysis
... Personal preference? ...
written 6 weeks ago by russhh2.7k
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Comment: C: GEO2R - significantly DEGs
... You have to be careful with your wording here: When you say that the data is normally distributed following log-transformation, do you mean the 'distribution of intensities across all probes for a given sample' or the 'distribution of intensities for a given probe across all samples' was normally ...
written 6 weeks ago by russhh2.7k
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Comment: C: GEO2R - significantly DEGs
... Would following the author's protocols for working with the raw data be of much value if the data have been transformed before upload to GEO? I'd strongly suggest that OP reads some of the metadata for the GSMxxxx files first to work out what manipulations were performed before upload. ...
written 6 weeks ago by russhh2.7k
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Comment: C: GEO2R - significantly DEGs
... Could you expand on the reasoning that led to you log-transforming the dataset, please. That is, what was it about the "distribution of the data in the Value Distribution section" that led you to log-transforming? There's a couple of flags in there for me: The box-plot given within the Value Distr ...
written 6 weeks ago by russhh2.7k

Latest awards to russhh

Scholar 10 days ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 23 days ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Scholar 7 weeks ago, created an answer that has been accepted. For C: muTect analysis, error
Scholar 9 weeks ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Appreciated 4 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Scholar 4 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 5 months ago, created an answer that has been accepted. For C: muTect analysis, error
Scholar 5 months ago, created an answer that has been accepted. For C: muTect analysis, error
Scholar 6 months ago, created an answer that has been accepted. For A: scripting problem to use ProtComp output to identify secretome proteins
Pundit 8 months ago, created a comment with more than 10 votes. For C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Scholar 8 months ago, created an answer that has been accepted. For A: scripting problem to use ProtComp output to identify secretome proteins
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Scholar 14 months ago, created an answer that has been accepted. For A: scripting problem to use ProtComp output to identify secretome proteins
Appreciated 14 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test

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