User: russhh

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russhh3.6k
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@haematobot
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Bioinformatics etc of leukaemia at University of Glasgow
 

Posts by russhh

<prev • 553 results • page 1 of 56 • next >
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Comment: C: R Model Matrix has extra columns
... it doesn't really make any difference (although it might make things simpler to reason about) since you specify the experimental comparisons in your contrasts matrix, not your design matrix ...
written 8 days ago by russhh3.6k
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Answer: A: R Model Matrix has extra columns
... your crelox column is stored as a `factor`. model.matrix will automatically put in a column for all non-reference levels of a factor variable, even if there isn't a sample with a given factor level. To mitigate against problems like this, you could use [droplevels][1] on your original dataframe ...
written 9 days ago by russhh3.6k
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Comment: C: Imbalance up and down regulated genes
... Could you repost that and only highlight the 38 downregulated and the 1345 upregulated features. There's looks like a fairly even directional balance above mean ~ 100 normalised counts. ...
written 10 days ago by russhh3.6k
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Comment: C: Imbalance up and down regulated genes
... could you post an MA plot ...
written 11 days ago by russhh3.6k
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Comment: C: Imbalance up and down regulated genes
... I've seen this before and it's always something to worry about. However, I've also seen it when analysing a dataset where an inhibitor of a global repressor of expression has been used - and it was consistent with other similar datasets. You've got to wonder whether there is real biology going on, ...
written 11 days ago by russhh3.6k
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Comment: C: Why I can't reproduce this heat map
... You still haven't defined what it is about the plot that you have generated that you want to fix so that it looks more like the plot in the paper. You have the same time trend but different data. If it were me, I'd drop the hierarchical stuff and order the genes by the time at which they display ma ...
written 12 days ago by russhh3.6k
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Comment: C: DESeq2 Error while applying standard analysis
... That's happened because you told it to happen here: `DESeq.ds_lusc_luad <- DESeqDataSetFromMatrix(countData= raw_reads_lusc_luad, colData = pheno_lusc_luad , design = ~1)` tcga lung is a pretty difficult dataset. ...
written 12 days ago by russhh3.6k
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Comment: C: Why I can't reproduce this heat map
... unless you've used exactly the same protocol as in the paper, the plot will be different. Unless the clusters are really well defined, heatmaps can be pretty flaky: adding a bit of noise to each entry will give you a different clustering. ...
written 12 days ago by russhh3.6k
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Comment: C: Why I can't reproduce this heat map
... plot looks fine to me ...
written 13 days ago by russhh3.6k
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Comment: C: How to work out degree exponent for protein-protein interaction networks (cyctos
... Isn't 'b' the degree-exponent? ...
written 17 days ago by russhh3.6k

Latest awards to russhh

Appreciated 11 weeks ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 11 weeks ago, created an answer that has been accepted. For C: muTect analysis, error
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 4 months ago, created an answer that has been accepted. For C: muTect analysis, error
Popular Question 5 months ago, created a question with more than 1,000 views. For Has the RNA-Seq Atlas website closed?
Popular Question 7 months ago, created a question with more than 1,000 views. For VariantAnnotation parallel usage
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Appreciated 7 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 7 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 C: muTect analysis, error
Appreciated 9 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Scholar 10 months ago, created an answer that has been accepted. For C: muTect analysis, error
Scholar 10 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 12 months ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 12 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Scholar 13 months ago, created an answer that has been accepted. For C: muTect analysis, error

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