User: elizabethR

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elizabethR70
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Posts by elizabethR

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Query about gene ontology analysis in edgeR vs GSEA
... thank you Gordon that is much appreciated ...
written 7 months ago by elizabethR70
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Query about gene ontology analysis in edgeR vs GSEA
... Hi I cannot find any similar posts to this on the forum, so please may I ask if anyone can help me? I have run differential expression on edgeR. I noted that edgeR has a gene ontology and KEGG pathway analysis function so I used it with the code from the users guide and vignette. I downloaded the ...
edger go written 7 months ago by elizabethR70
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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 21 months ago by elizabethR70
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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 21 months ago by elizabethR70 • updated 21 months ago by Kevin Blighe49k
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Comment: 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 2.1 years ago by elizabethR70
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Comment: 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 2.1 years ago by elizabethR70
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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 2.1 years ago by elizabethR70
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input counts to PCA in RNAseq
... Hi 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 data. Should I input raw ...
R ggplot2 pca rna-seq written 2.1 years ago by elizabethR70 • updated 7 months ago by Kevin Blighe49k
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Answer: A: Gene symbol for original TCGA data ...help!
... Thank you that's incredibly helpful! ...
written 2.1 years ago by elizabethR70
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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 2.1 years ago by elizabethR70

Latest awards to elizabethR

Popular Question 7 months ago, created a question with more than 1,000 views. For RNASeq TCGA data
Student 7 months ago, asked a question with at least 3 up-votes. For input counts to PCA in RNAseq
Popular Question 21 months ago, created a question with more than 1,000 views. For How to plot RNASeq data in PCA
Popular Question 21 months ago, created a question with more than 1,000 views. For RNASeq TCGA data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How to set up TCGAbiolinks in R studio?

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