User: elizabethR

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elizabethR30
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Posts by elizabethR

<prev • 15 results • page 1 of 2 • next >
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Comment: C: WGCNA Difficulty in making clinical trait data file to match cluster-filter samp
... That doesn't work either, all I have is a column of numbers from 1 to 31 (for number of samples) and an empty column next to it that says NA in it. I do not have sufficient coding knowledge to know how to fix this myself. I am perplexed that the r coding in the WGCNA handbook would be so redundant ...
written 15 days ago by elizabethR30
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WGCNA Difficulty in making clinical trait data file to match cluster-filter samples
... Hi I would be very grateful for some help. I am trying to use WGCNA to perform network analysis on TCGA RNASeq data. I am at the Data Input and Cleaning stage, after using clustering to exclude outlying samples I am having difficulty making my clinical trait data to align and match with my RNAS ...
wgcna rownames written 16 days ago by elizabethR30 • updated 15 days ago by Kevin Blighe11k
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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 4 months 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 4 months 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 4 months 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 4 months 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 4 months ago by elizabethR30
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Answer: A: Gene symbol for original TCGA data ...help!
... Thank you that's incredibly helpful! ...
written 4 months 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 4 months 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 4 months ago by elizabethR30

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