User: chris86

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chris86240
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240
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Location:
UCL, United Kingdom
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10 hours ago
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1 year, 6 months ago
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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 • 117 results • page 1 of 12 • next >
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Good to know ...
written 6 days ago by chris86240
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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 7 days ago by chris86240
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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 7 days ago by chris86240
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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 9 days ago by chris86240
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Comment: C: GO enrichment comparison with other programs
... OK thanks, that is interesting. ...
written 15 days ago by chris86240
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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 15 days ago by chris86240
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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 6 weeks ago by chris86240
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Comment: C: ConsensusClusterPlus - function "calcICL" - How the samples are ordered in the p
... hierarchical clustering of the consensus matrix ...
written 7 weeks ago by chris86240
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Comment: C: Test whether expression levels of two gene sets are significantly different
... Thanks for this point Gordon, I hadn't thought of that. ...
written 9 weeks ago by chris86240
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Comment: C: Test whether expression levels of two gene sets are significantly different
... No because they don't take into account length ...
written 9 weeks ago by chris86240

Latest awards to chris86

Scholar 9 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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