User: -_-

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-_-470
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Posts by -_-

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Comment: C: How to reproduce TCGA rsem values from firebrowse
... Hi @genomax, do you happen to know if the same pipeline has been applied to obtain expression values of samples any other cancer projects (e.g. CCLE), please? ...
written 7 weeks ago by -_-470
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Comment: C: CCLE RNA-seq library protocol
... Just to confirm, so CCLE mRNA dataset is non-stranded, right? ...
written 7 weeks ago by -_-470
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Comment: C: How to reproduce TCGA rsem values from firebrowse
... Thanks! Based on your link, I found a couple of very useful links: 1. A writeup of basically exactly the question I am facing: http://bsbludwig.com/post/94066296740/what-do-tcgas-rnaseq-files-actually-show#disqus_thread 2. More details about the UNC pipeline using RSEM: https://webshare.bioinf.unc. ...
written 7 weeks ago by -_-470
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How to reproduce TCGA rsem values from firebrowse
... I would like to apply TCGA's mRNA quantification pipeline to other samples, but I couldn't find detailed documentation about how their expression values are quantified? Here is what I know so far: rsem is used for expression quantification. What about the aligner (together with the parameters used ...
tcga rsem expression written 7 weeks ago by -_-470 • updated 7 weeks ago by genomax37k
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Answer: C: Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression d
... Here is the GDC page: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files, the TCGA.hg19.June2011.gaf is the same as @namshik.han's linked file ...
written 9 weeks ago by -_-470
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Comment: C: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
... I found that genes don't include all isoforms, which explains why isoform-level scaled estimates sum to 1 while gene-level scaled estimates don't. Details are in https://gitlab.com/zyxue/understanding-firebrowse-data-format/blob/master/confirm-relationship-between-gene-level-and-isoform-level-scaled ...
written 4 months ago by -_-470
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Comment: C: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
... @Mattias Aine, do you have any new insight on why the sum of fractions is not one and sum <0.8 is not uncommon, please? I have had the same observation. ...
written 4 months ago by -_-470
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Answer: A: How does deseq2 encode more than 2 levels
... >DESeq2 uses model.matrix so you can just plug your design and colData into this base R function to see how it will be encoded. Quoted from https://support.bioconductor.org/p/77620/#97059 > model.matrix(~participant+sampleType, coldata) (Intercept) participantX8326 parti ...
written 5 months ago by -_-470
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How does deseq2 encode more than 2 levels
... When there are two levels per factor, it could be encoded as 0 and 1. What about 3 factors, then? Is it one-hot encoding or something like that when DESeq fit a generalized linear model over the factors? I don't find such information in the [paper][1] or [user guide][2] yet. If you could even point ...
deseq2 rna-seq differential expression written 5 months ago by -_-470
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Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... I am looking at this http://firebrowse.org/, KICH, Mutation Annotation File, and I downloaded both Mutation_Packager_Calls (MD5) Mutation_Packager_Oncotated_Calls (MD5) But I only found MAF files for tumour samples, and couldn't find the corresponding MAFs file for normal samples. Any idea wher ...
normal firehose tcga mutation firebrowse written 6 months ago by -_-470

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