User: chris86
chris86 • 290
- Reputation:
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- UCL, United Kingdom
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.
Posts by chris86
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... The files you are looking for are here:
http://www.ebi.ac.uk/ena/data/view/PRJEB14614
You can start with the .fastq files from the FTP.
...
written 20 days ago by
chris86 • 290
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... You cant remove batch effects if the data is 100% confounded.
Better just to ignore the normals.
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written 22 days ago by
chris86 • 290
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... I remove outliers when there is something obviously amiss with that sample because something went wrong with the array or sample prep i.e. clustering gives some really weird outlier. Other than that, I leave them.
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written 28 days ago by
chris86 • 290
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... Hi
I am almost finished my package and the paper is nearly done too. Which order do I submit these in? Do I wait for it to be accepted by the bioconductor then submit to journal or vice versa?
Thanks,
Chris
...
written 29 days ago by
chris86 • 290
• updated 29 days ago by
Martin Morgan ♦♦ 20k
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... Hi
I was wondering if anyone could help me with the following. Of 353 detected miRNAs 74 were statistically significant (FDR 10%), if I recall correctly at 10% FDR I should expect 3.53 significant miRNAs, but what is the probability of observing 74 at this threshold. The FDR is calculated using ben ...
written 12 weeks ago by
chris86 • 290
• updated 12 weeks ago by
Gordon Smyth ♦ 30k
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... use limma and read the manual
...
written 4 months ago by
chris86 • 290
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... Just read some papers, e.g.
Anders, S. and Huber, W., 2012. Differential expression of RNA-Seq data at the gene level–the DESeq package. Heidelberg, Germany: European Molecular Biology Laboratory (EMBL).
Law, C.W., Chen, Y., Shi, W. and Smyth, G.K., 2014. Voom: precision weights unlock linear mode ...
written 4 months ago by
chris86 • 290
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... http://deweylab.biostat.wisc.edu/rsem/README.html. Colin who developed RSEM recommends using EBSEQ. That is the answer for this specific problem.
We always used to use rounded counts in DESEQ, it used to upset the statistics guy, but we ignored him.
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written 5 months ago by
chris86 • 290
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... You can round them and use in DESEQ2, but that isn't recommended and people normally use a specific tool that can cope with the uncertainty of read count estimates like EBSEQ.
...
written 5 months ago by
chris86 • 290
Latest awards to chris86
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15 days ago,
created a question with more than 1,000 views.
For Limma camera function never gives any differentially expressed gene sets
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14 months ago,
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For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
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14 months ago,
created 100 posts.
Scholar
14 months ago,
created an answer that has been accepted.
For A: Heatmap of a subset of genes
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For Limma camera function never gives any differentially expressed gene sets
Scholar
14 months ago,
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For A: Heatmap of a subset of genes
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