Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe33k
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Republic of Ireland
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'Incrocio le dita e spero'

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Developer / Maintainer of Bioconductor packages:

Posts by Kevin Blighe

<prev • 4,864 results • page 2 of 487 • next >
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Comment: C: [TCGA] Variant caller used in mutation data of TCGA
... I would contact the RTCGAToolbox developers ...
written 2 days ago by Kevin Blighe33k
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Comment: C: Refseq accessions - getting gene function and GO terms for each one
... Which gff do you have? Please paste some entries from it, and wrap the output with the `101 010` button ...
written 2 days ago by Kevin Blighe33k
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Comment: C: Problem in using TCGAvisualize_meanMethylation function
... I have reproduced the error on my computer. From where did you obtain the code? ...
written 2 days ago by Kevin Blighe33k
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Comment: C: WGCNA soft thresholding problem
... Strange, and unfortunate! By all means you can still use the unlogged, normalised EdgeR counts; however, just clearly state this in the methods. As WGCNA is based on correlation, logged or unlogged counts should be fine (and this is stated by the developer(s) of the program). I say all of this with ...
written 2 days ago by Kevin Blighe33k
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Comment: C: Problem in using TCGAvisualize_meanMethylation function
... I tidied your code to improve the visualisation of it. From where did you obtain this code? There are many 'bugs' (errors) with TCGAbiolinks. ...
written 2 days ago by Kevin Blighe33k
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Comment: C: Problem in using TCGAvisualize_meanMethylation function
... You are not the person who opened this question; thus, your problem is likely different. Which error message are you receiving? ...
written 2 days ago by Kevin Blighe33k
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Comment: C: Healthy controls - samples Illumina 450k methylation
... Can you provide direct links to the data and the published manuscripts pertaining to these? ...
written 2 days ago by Kevin Blighe33k
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Comment: C: Getting unusual characters while generating output files in a bash script
... I agree - this looks like a job for `dos2unix`, a very useful tool too have. The solutions found through Pierre's links are also plausible. `\r` is an end-line character. Another commonly-found one is `^M`. ...
written 2 days ago by Kevin Blighe33k
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Comment: C: GDCprepare stop working for some unknown reason
... Cross-posted: https://support.bioconductor.org/p/115959/ ...
written 3 days ago by Kevin Blighe33k
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Comment: C: WGCNA soft thresholding problem
... If I am honest, I would take the edgeR data and go with it. Look at it this way: if you state in your methods that you used EdgeR normalised counts as input to WGCNA, I am doubtful that many would disagree. For the boxplot, it is typical to have outliers like that with RNA-seq data. You could set ` ...
written 3 days ago by Kevin Blighe33k

Latest awards to Kevin Blighe

Librarian 1 day ago, created a post with more than 10 bookmarks. For Network plot from expression data in R using igraph
Prophet 1 day ago, created a post with more than 20 followers. For Network plot from expression data in R using igraph
Scholar 3 days ago, created an answer that has been accepted. For A: How to change conditions in DESeq2
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Popular Question 7 days ago, created a question with more than 1,000 views. For R functions edited for parallel processing
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Scholar 9 days ago, created an answer that has been accepted. For A: How to change conditions in DESeq2
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
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Good Answer 13 days ago, created an answer that was upvoted at least 5 times. For A: cox proportional hazard model
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Great Question 16 days ago, created a question with more than 5,000 views. For Network plot from expression data in R using igraph
Scholar 20 days ago, created an answer that has been accepted. For A: How to change conditions in DESeq2
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