User: Fiona

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Fiona70
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Posts by Fiona

<prev • 13 results • page 1 of 2 • next >
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Normalisation of RNA seq data
... Hi everyone, I'm struggling to understand pros and cons of various ways of normalising RNA-seq read count data. Although I'm not working with a specific dataset at the moment, in theory I'm thinking about read counts from replicated samples, and trying to test differential expression between diffe ...
rnaseq normalization R bioconductor written 3.2 years ago by Fiona70 • updated 3.2 years ago by chris86380
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DEXSeq analysis of alternative splicing: error 'SAM optional field tag NH not found'
... Dear All, I am attempting to use DEXSeq version 1.14.2 to analyse alternative splicing in my RNA-seq data. Generally, I am pretty comfortable in R and try to keep my analyses in R, but the initial steps of the DEXSeq pipeline (as described in the 2015 vignette for version 1.14.2 by Reyes et al) inv ...
dexseq splicing sam python written 3.5 years ago by Fiona70
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Comment: C: RNA-seq analysis with R/BioC: alignment and read counts
... Thanks for pointing this out - I didn't know about the makeTxDbFromUCSC function, and it fixes the problem. ...
written 3.8 years ago by Fiona70
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Comment: C: RNA-seq analysis with R/BioC: alignment and read counts
... Thank you for the code and for the explanation! This makes sense, and the code fixes the problem. ...
written 3.8 years ago by Fiona70
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Comment: C: RNA-seq analysis with R/BioC: alignment and read counts
... Thanks very much for the suggestion - I didn't realize limma could be used for RNAseq as well as microarray analysis, so this will definitely be worth me trying out. ...
written 3.8 years ago by Fiona70
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RNA-seq analysis with R/BioC: alignment and read counts
... Hi everyone, I'm analyzing my first paired-end RNA-seq data in R/BioConductor and I'm having some trouble. I've given detail below but please let me know if I need to give more information. I'd be really grateful for any help or pointers. I downloaded the D. melanogaster reference genome (dm6, the ...
alignment drosophila melanogaster genomicfeatures genomicranges quasr written 3.8 years ago by Fiona70 • updated 3.8 years ago by Hervé Pagès ♦♦ 13k
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Answer: A: Regarding CDF file
... Dear Deepika, I had a similar problem when using Affy microRNA arrays. I emailed Affymetrix support at supporteurope@affymetrix.com although note that there are different email addresses depending on where you are based - the information is all on their website (http://www.affymetrix.com/about_af ...
written 5.9 years ago by Fiona70
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tutorials for RNA-seq analysis in Bioconductor
... Hi everyone, Quick question: can anyone recommend tutorials/resources which are available online that I could use to get started with the basics of analysing RNA-seq data in Bioconductor? I've come across a few things (sets of lecture slides and sets of code to work through) but I just thought I wo ...
alignment written 5.9 years ago by Fiona70 • updated 5.9 years ago by Steve Lianoglou12k
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identifying drosophila miRNA targets
... This is great! This seems to be running fine now and the results are making more sense. I hoped the problem was something to do with not having all my lists of RNAs in the right format, but working out how to code the conversion was beyond me, so thanks very much for taking the time to work that thr ...
mirna drosophila2 probe affy convert affycoretools microrna written 6.1 years ago by Fiona70
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Comment: C: identifying drosophila miRNA targets
... Hi Jim, Thanks very much for pointing that out - it seems mirna2mrna is exactly what I was after, I don't know how I managed to overlook it . I'm a bit puzzled about the results I'm getting, however, and so if you have a minute to think this through then I'd be really grateful. The help pages are ...
written 6.1 years ago by Fiona70

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