User: andresllucena

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Posts by andresllucena

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How can I identify and remove outliers samples based on a MDS plot (limma package)?
... Hi, I downloaded microRNA expression data from TCGA (Isoform Expression Quantification files) using the TCGAbiolinks package from Bioconductor. Now I made a MDS plot using limma package function `plotMDS` but I have a weird distance between samples of same group (normal tissue group) and called it o ...
R tcga limma edger rna-seq written 5 weeks ago by andresllucena0 • updated 5 weeks ago by seidel7.4k
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Comment: C: How do i create and populates new sample columns based on values (samples barco
... I'm sorry, I will correct that. I used values from samples after the first one trying to improve the example. Thank you so much. P.S.: function `pivot_wider` seem to be from tidyr package and not dplyr. ...
written 6 weeks ago by andresllucena0
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How do i create and populates new sample columns based on values (samples barcodes) from an existing column
... I have a data frame as follows: miRNA_region barcode read_count MIMAT0000062 TCGA-05-4244-01A-01T-1108-13 14492 MIMAT0000063 TCGA-05-4244-01A-01T-1108-13 8767 MIMAT0000064 TCGA-05-4244-01A-01T-1108-13 610 MIMAT0000065 TCGA-05-4244-01A ...
R tcga written 6 weeks ago by andresllucena0
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Answer: A: Identifying 5p and 3p in miRNA isoform expression data from TCGA for feature sel
... There is how i solve that: The 3p and 5p strands corresponds to these MIMAT IDs miRNA_region column, then you'll have to sum counts with this same ID for each sample and then you'll have the raw counts that you need for differential expression analysis and so on. First, delete rows of ''precursor' ...
written 6 weeks ago by andresllucena0
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Comment: C: How to use genewise using pubmed.mineR ?
... yes it does http://ramuigib.blogspot.com/ ...
written 5 months ago by andresllucena0

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