User: emmapead2

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emmapead260
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Posts by emmapead2

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Oligo and Limma
... Is your normalised data of class ExpressionSet? If so, carry on and use limma. Look at the documentation for examples. https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/intro.pdf ...
written 3.4 years ago by emmapead260
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Answer: A: FastQC on rna-seq data
... I would use trim galore eg. trim_galore --phred64 --paired --trim1 *fastqc ...
written 3.4 years ago by emmapead260
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Comment: C: How do scientists identify new genes/SNP as candidates for GWAS studies?
... Oh cool, thats good to know, I may have to start using VEP! ...
written 3.4 years ago by emmapead260
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Comment: C: How do scientists identify new genes/SNP as candidates for GWAS studies?
... VEP does the same as snpEff, so it just depends on what other tools you are using (for compatibility). ...
written 3.5 years ago by emmapead260
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Answer: A: Origin of SNP of interest
... This might be helpful http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-162 ...
written 3.5 years ago by emmapead260
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Answer: A: How do scientists identify new genes/SNP as candidates for GWAS studies?
... I may be looking at this wrong but if I was in the scenario that I had a sequence from a diseased patient, then identified the SNP's in this sequence I would then use snpeff to annotate the predicted effect of the SNP (synonymous/non-synonymous). This would give me a loci for the gene. I could then ...
written 3.5 years ago by emmapead260
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Comment: C: How to stop R creating syntactically correct names
... Thanks very much, I'll give it a go. Just strange how check.names = F regardless of which package I use to bring in the file just does not work at all, especially if their are replicates. Which is a major issue as I need to keep them but also be able to trace back their corresponding values which I' ...
written 3.5 years ago by emmapead260
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Comment: C: How to stop R creating syntactically correct names
... I've tried this already but make.names does not like replicates. It will add ".1" on the end. This is still an issue as I'm comparing multiple sets which may have the same metabolites and comparing e.g L.Leucine.1 in one file to L.Leucine.1 in another does not necessarily mean they are identified as ...
written 3.5 years ago by emmapead260
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Comment: C: How to stop R creating syntactically correct names
... I may try there, but thought I'd post on here just in case anyone has done this kind of analysis with metabolomics data specifically and may have advice. ...
written 3.5 years ago by emmapead260
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Comment: C: How to stop R creating syntactically correct names
... Ahhhhhh so I think my problem has been is that I'm actually reading it from excel (nobody shout at me, I was given the data like this :D) so it stores the names of my metabolites as row names which really need to be different for anything further to work. So I guess if I just store my metabolites as ...
written 3.5 years ago by emmapead260

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