User: chris86

gravatar for chris86
chris86260
Reputation:
260
Status:
Trusted
Location:
UCL, United Kingdom
Last seen:
16 hours ago
Joined:
1 year, 10 months ago
Email:
c*************@gmail.com

I am a post-doc data analyst working in Rhuematoid Arthritis research at UCL, London. I am working with data from multiple genomic platforms and experimental types and we are trying to integrate this data to provide more personalised treatments.

Posts by chris86

<prev • 121 results • page 1 of 13 • next >
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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 16 hours ago by chris86260 • updated 13 hours ago by Martin Morgan ♦♦ 19k
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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 8 weeks ago by chris86260 • updated 8 weeks ago by Gordon Smyth30k
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Comment: C: illumina ht-12 v4 expression beadchip
... use limma and read the manual ...
written 3 months ago by chris86260
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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 3 months ago by chris86260
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Good to know ...
written 4 months ago by chris86260
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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 4 months ago by chris86260
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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 4 months ago by chris86260
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Comment: C: Finding specific modules compared to consensus modules; cut-off?
... There should be a p value from the cross tabulation results from the module preservation in WGCNA, you have to look for that, you only have number of genes overlapping... ...
written 4 months ago by chris86260
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Comment: C: GO enrichment comparison with other programs
... OK thanks, that is interesting. ...
written 4 months ago by chris86260
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Comment: C: GO enrichment comparison with other programs
... Not quite sure why you would bother doing this because these functional enrichment tests/ packages are usually the same and based on hypergeometric distribution, the issue is just using a package that updates its definitions of KEGG or GO pathways etc. I use cluster profiler and find it very helpful ...
written 4 months ago by chris86260

Latest awards to chris86

Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.
Student 13 months ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Supporter 13 months ago, voted at least 25 times.
Scholar 13 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Centurion 13 months ago, created 100 posts.
Scholar 13 months ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Scholar 13 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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