User: lykosherdshep

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Posts by lykosherdshep

<prev • 16 results • page 1 of 2 • next >
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Comment: A: How to acquire the mature miRNA data from TCGA
... Or if there are another method? ...
written 8 days ago by lykosherdshep10
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How to acquire the mature miRNA data from TCGA
... Hello! I have some questions about the data from TCGA(experimental.strategy = "miRNA-Seq"), there are two data types "miRNA Expression Quantification" and "Isoform Expression Quantification". I have read GDC data user guide which says that The former contains summed expression for all reads aligned ...
tcga rna-seq mirna written 8 days ago by lykosherdshep10
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Comment: C: SVA Input: Should SVs be calculated on normalized data?
... I'm meeting the seem question, you can have a look at https://www.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#pre-filtering-the-dataset where sva input takes a normalized counts through counts(data, normalized = T) ...
written 19 days ago by lykosherdshep10
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Comment: C: How to import RSEM expected_count data in ucsc to a deseq2 object ?
... Thanks for your recommendation, I find another way in rsem official site-"ebseq" package, I'll try the both. ...
written 24 days ago by lykosherdshep10
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How to import RSEM expected_count data in ucsc to a deseq2 object ?
... I have downloaded gene expression data frome https://xenabrowser.net/datapages/?dataset=TcgaTargetGtex_gene_expected_count&host=https%3A%2F%2Ftoil.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443, I find the unit of the data is log2(expected_count+1),and I want to use t ...
rna-seq written 26 days ago by lykosherdshep10
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the selection between legacy archive and harmonization in TCGA when compared to GTEx in the differential expression analysis
... I want to do a differential expression analysis between prostate cancer and normal tissue with the former RNA-seq read counts from TCGA and the latter RNA-seq read counts from GTEx. I realize the workflow of RNA-seq and alignment difference may cause problem. I find TCGA has two different part-Legac ...
rna-seq written 27 days ago by lykosherdshep10
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Comment: C: How to deal with the abnormal samples from TCGA found in a PCA?
... Thanks very much, I read what you have said again, and I think I have understood what you explain. Thank you for removing my confussion. ...
written 4 weeks ago by lykosherdshep10
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Comment: C: How to deal with the abnormal samples from TCGA found in a PCA?
... Thanks for your patient explanation, can I have this understanding that it's the number of the normal samples in TCGA database that mainly restrict the use to differential expression gene in TCGA and the quality of the normal samples? is it right? I'm a beginner in bioinformatics, and I'm also a st ...
written 4 weeks ago by lykosherdshep10
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Comment: C: How to deal with the abnormal samples from TCGA found in a PCA?
... Thanks for you to tell me these, I am still confused, I still don’t know the necessity of choosing the true normal samples, Could you tell me some reasons for it? ...
written 4 weeks ago by lykosherdshep10
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Comment: C: How to deal with the abnormal samples from TCGA found in a PCA?
... I'm a bit confused about the control samples selection between a true normal sample with tissue from a no-cancer individual and a normal tissue from a cancer people for RNA-seq, I can understand it is a better choice to chose a true normal sample from what you said, but in my opinion, it may be good ...
written 4 weeks ago by lykosherdshep10

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