User: chris86

gravatar for chris86
chris86260
Reputation:
260
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Trusted
Location:
UCL, United Kingdom
Last seen:
2 hours ago
Joined:
1 year, 8 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 • 120 results • page 1 of 12 • next >
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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 1 day ago by chris86260 • updated 1 day ago by Gordon Smyth30k
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Comment: C: illumina ht-12 v4 expression beadchip
... use limma and read the manual ...
written 5 weeks 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 6 weeks 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 11 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by chris86260
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Comment: C: GO enrichment comparison with other programs
... OK thanks, that is interesting. ...
written 12 weeks 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 12 weeks ago by chris86260
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Comment: C: Problem with Combat batch adjustment
... You cannot use COMBAT when your data is 100% confounded like that. I have the same problem, because everything was done in the same lab and same platform and same people for me we are just assuming batch effect does not exist. This is bad experimental design. ...
written 3 months ago by chris86260

Latest awards to chris86

Autobiographer 10 months ago, has more than 80 characters in the information field of the user's profile.
Student 11 months ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Supporter 11 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Centurion 11 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Scholar 11 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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