User: russhh

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russhh4.1k
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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 • 610 results • page 1 of 61 • next >
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Comment: C: Can anybody explain me why this volcano plot is not opening
... looks like you've got a consistently higher signal in one set of samples than the other. How did you normalise the (microarray?) dataset? ...
written 7 weeks ago by russhh4.1k
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Comment: C: How to extract unique values between columns in R ?
... Your output isn't a data-frame, it has different vector lengths for each entry. Could you confirm why 13 is in the output for `B` given that it was absent from the input; and why 35 was filtered out of column C given that it is absent from column A. You might be better to generate a data.frame wit ...
written 10 weeks ago by russhh4.1k
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Answer: A: Deseq2 - Log2FoldChange is dependent on the number of genes in the analysis
... Library size is dependent upon the genes included. In the simplest setting, for a given gene in a given sample the negative-binomial model effectively models the number of counts observed (for that gene) relative to the number of reads observed in total (for that sample). If you change the library s ...
written 10 weeks ago by russhh4.1k
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Comment: C: Microaaray data analysis
... Disease association doesn't really imply disease involvement. And you have to be able to reproducibly show that your genes are discriminatory or you multi-gene signature is valid before you get to call them/it a biomarker. Depending on the application (early detection, prognosis, ...), very few biom ...
written 10 weeks ago by russhh4.1k
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Comment: C: mutual rank values for distance matrix formation for co-expression analysis
... why can't you just use the MR values as a distance? It might not be subadditive ...
written 11 weeks ago by russhh4.1k
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Comment: C: Cooperation for scientific project (python, deep learning, image recognition, hi
... could you post a bit more detail regarding your own research background, where the project will be based, whether the student will need to secure their own funding, whether they can work at-distance, please. ...
written 11 weeks ago by russhh4.1k
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Comment: C: DESeq2:Why is there an oblique line in my MA picture, which happened before, wha
... are there differences in the library-sizes between your treatment-groups? ...
written 11 weeks ago by russhh4.1k
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Answer: C: Extracting rows in r by their number
... if you have `rows <- c(100, 876, 438, ... 997 other entries ...)` then `my_matrix[rows, ]` is how you 'submatrix-by-row-index'. In R you can index by either rownames or indices, or a boolean 'mask' vector (here it would be a vector of FALSEs with TRUE at the 100th, 438th, 876th and the other 997 ...
written 11 weeks ago by russhh4.1k
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Comment: C: Correlation between lncRNA and protein coding genes
... my_cor <- apply(my_cpm, 1, function(x){cor(x,count["ENSG00000000005.5",], method = "spearman")}) I don't think plotting the correlation coefs would be particularly revealing; but you can do it if you want ...
written 11 weeks ago by russhh4.1k
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Comment: C: Correlation between lncRNA and protein coding genes
... Set the `method` argument. See here: https://www.rdocumentation.org/packages/stats/versions/3.5.1/topics/cor ...
written 11 weeks ago by russhh4.1k

Latest awards to russhh

Scholar 8 weeks ago, created an answer that has been accepted. For C: muTect analysis, error
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Has the RNA-Seq Atlas website closed?
Scholar 8 weeks ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 12 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
Scholar 3 months ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 4 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Appreciated 5 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Appreciated 8 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Scholar 8 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 9 months ago, created an answer that has been accepted. For C: muTect analysis, error
Popular Question 11 months ago, created a question with more than 1,000 views. For Has the RNA-Seq Atlas website closed?
Popular Question 12 months ago, created a question with more than 1,000 views. For VariantAnnotation parallel usage
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Appreciated 13 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples

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