User: -_-

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-_-470
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Posts by -_-

<prev • 42 results • page 1 of 5 • next >
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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 2 days 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 11 weeks 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 11 weeks 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 3 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 3 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 4 months ago by -_-470
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Comment: C: Normal blood RNA-Seq data from cancer (any cancer) patients
... thanks, tried, no luck. ...
written 5 months ago by -_-470
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Normal blood RNA-Seq data from cancer (any cancer) patients
... Is anyone aware of any publically available RNA-Seq dataset of normal blood tissue but from cancer (any cancer but leukemia) patients, please? ...
normal blood rna-seq cancer written 5 months ago by -_-470
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... Thanks. My confusion mainly came from if BAM is 0-based, then it would make more sense if SAM is also 0-based since the two are essentially the same except for one is compressed while the other is not. But as you explained, if that's not case, it's very unintuitive to me, but very good to know. ...
written 5 months ago by -_-470
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... Is it true that SAM is 1-based but BAM is 0-based? Why would it be designed this way? ...
written 5 months ago by -_-470

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Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Insert Size And Fragment Size ?
Scholar 3 months ago, created an answer that has been accepted. For A: How does deseq2 encode more than 2 levels
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