User: aluesley1

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aluesley140
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Posts by aluesley1

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Comment: C: Matched paired DEA analysis of BRCA samples using TCGAbiolinks, works for paired
... Thank you so much for this. It's a bit frustrating and misleading that it's not a true paired analysis and I appreciate the time you have put into checking this is the case. I'm going to have an attempt to perform the analysis myself using edgeR as it is part of my MSc research project and I would ...
written 5 months ago by aluesley140
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Comment: C: Matched paired DEA analysis of BRCA samples using TCGAbiolinks, works for paired
... Hello! Yes it is a continuation from that. I used a workflow for TCGAbiolinks to process the matched data. I have used it before for unmatched normal-tumour samples and it has worked. Here is what I have used - Matched.Samples.Normal <- subset(prep.BRCA.normal, ...
written 5 months ago by aluesley140
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Matched paired DEA analysis of BRCA samples using TCGAbiolinks, works for paired = FALSE but not paired = TRUE
... I am attempting to do a DEA analysis of matched paired BRCA normal tumour samples using TCGAbiolinks. When I do an analysis of my samples using this formula dataDEGsMatched <- TCGAanalyze_DEA(mat1 = MatchedTPdataFilt, mat2 = MatchedNTdataFilt, ...
tcgabiolinks R rna-seq written 5 months ago by aluesley140 • updated 5 months ago by Kevin Blighe33k
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Comment: C: Matched Paired Tumour-Normal DEA of BRCA using data downloaded using TCGAbiolink
... Ah thank you so much, such a silly error! When I used GDCDataCommons to identify files for matched paired samples for gene expression it came back with 112 but using the correct code with TCGAbiolinks find 113 which is a bit confusing. ...
written 5 months ago by aluesley140
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Matched Paired Tumour-Normal DEA of BRCA using data downloaded using TCGAbiolinks
... I am trying to use BRCA data downloaded using TCGAbiolinks to do a differential expression analysis. I want to do an analysis of the matched-paired tumour-normal samples but can't work out how to identify these cases from the samples I have. This is the code I have so far and my attempt to subset ...
tcgabiolinks R tcga written 5 months ago by aluesley140 • updated 5 months ago by Kevin Blighe33k
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Subsetting a RangedSummarizedExperiment in R
... Hi, sorry if this is a bit basic but I'm very new to R. I am working in Rstudio and I have gene expression data downloaded using TCGAbiolinks, I have downloaded it and prepared it into a RangedSummarizedObject so it includes the clinical data. I want to subset the data based on this clinical data ...
tcgabiolinks R rangedsummarizedexperiment written 6 months ago by aluesley140 • updated 6 months ago by Friederike2.3k

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