User: elizabethR

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elizabethR30
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Posts by elizabethR

<prev • 13 results • page 1 of 2 • next >
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Answer: A: RNASeq TCGA data
... Thank you. To date I have been using the raw (aligned) counts from the rsem.genes (non normalised) RNASeqV2 total RNA data files. I had assimilated them from cancer and normal tissue samples to do DE analysis using edgeR... is that ok? ...
written 7 days ago by elizabethR30
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Answer: A: Help! How to plot RNASeq data in PCA
... I am not familiar with DESeq2, I have been using edgeR up to now. I have just been reading the manuals and online tutorials and looking at how to input the data. I see it will accept a count matrix such as the one I have in csv format, but that it needs a metadata file. I am really not sure how to m ...
written 11 days ago by elizabethR30
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RNASeq TCGA data
... Hey I have been analysing some of the RNASeq data from TCGA. I have been using total RNA files from RNASeqV2 on the advice of my supervisor. However there are also other types of RNASeq, including exons, splice junctions and isoforms. I've not been able to find somewhere that explains what you can ...
tcga rna-seq written 11 days ago by elizabethR30
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Answer: A: Help! How to plot RNASeq data in PCA
... Thank you that's really really helpful :) ...
written 11 days ago by elizabethR30
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Help! How to plot RNASeq data in PCA
... Hi! Could I ask advice? I would like to plot RNASeq data that I have downloaded from TCGA in a PCA plot. I have found some great guides on how to plot the actual data in PCA using r in ggplot2 and such but my main question is what format data should I plot? I currently have raw counts and RSEM d ...
pca rna-seq written 12 days ago by elizabethR30
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Answer: A: Gene symbol for original TCGA data ...help!
... Thank you that's incredibly helpful! ...
written 19 days ago by elizabethR30
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Comment: C: Gene symbol for original TCGA data ...help!
... Yes, FAM38A is now Piezo1 for instance. When I ran the data through WebGestalt it couldnt map 1338 of the genes and eyeballing them it looks like their gene symbols have changed. ...
written 24 days ago by elizabethR30
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Gene symbol for original TCGA data ...help!
... Hi all I have been on maternity leave for a year prior to which I was analysing TCGA RNASeq cancer data, which I downloaded, collated and analysed. I have been trying to run some new analyses now IM back at work but the gene symbol names have changed that Im looking at! I tried to run GSEA in WebG ...
tcga genesymbol written 25 days ago by elizabethR30
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Answer: A: Analysing gene expression across clinical parameters
... Thank you guys, EagleEye that link was very useful. EdgeR manual says you should use raw counts that haven't been normalised because it's normalised and log transformed as part of its mathematical modelling. I've used edgeR to perform differential expression analysis across clinical parameters ...
written 15 months ago by elizabethR30
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Answer: A: Genomic Matrix data from TCGA need to be analysied for Differential gene express
... Ive been told by a bioinformatician to use EdgeR to do differential expression analysis. However as I understand it this data cannot be normalised, has to be raw counts (i.e. rsem.genes.results files rather than the normalised files because edgeR normalises it as part of its mathematical modelling ...
written 15 months ago by elizabethR30

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