User: chris86

gravatar for chris86
chris86290
Reputation:
290
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Trusted
Location:
UCL, United Kingdom
Last seen:
1 day, 12 hours ago
Joined:
1 year, 11 months ago
Email:
c*************@gmail.com

I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 124 results • page 1 of 13 • next >
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Answer: A: Which raw files (RNAseq) to download?
... 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 chris86290
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Answer: A: gene expression data analysis and batch effect methods
... You cant remove batch effects if the data is 100% confounded. Better just to ignore the normals. ...
written 22 days ago by chris86290
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Answer: A: Outliers - to remove or to not remove that is the question
... 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. ...
written 28 days ago by chris86290
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How does it work with submitting a package to the bioconductor and doing the paper together?
... 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 ...
bioconductor written 29 days ago by chris86290 • updated 29 days ago by Martin Morgan ♦♦ 20k
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Calculating probability of getting xx genes past FDR10%
... 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 ...
limma written 12 weeks ago by chris86290 • updated 12 weeks ago by Gordon Smyth30k
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Comment: C: illumina ht-12 v4 expression beadchip
... use limma and read the manual ...
written 4 months ago by chris86290
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Comment: C: Negative bionomial model (test) vs T test in EBseq or DEseq2
... 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 chris86290
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Good to know ...
written 5 months ago by chris86290
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... 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. ...
written 5 months ago by chris86290
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... 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 chris86290

Latest awards to chris86

Popular Question 15 days ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 13 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 14 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Centurion 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
Student 14 months ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 14 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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