User: magicpants

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magicpants60
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Posts by magicpants

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... should be the `cpm()` function? ...
written 2 days ago by magicpants60
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... What if I need something accounts for gene length and intersample differences? Could I do between sample normalization, like TMM, on TPM values? ...
written 5 days ago by magicpants60
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Answer: A: genefu for PAM50 prediction
... Values that have been normalized and transformed for between sample comparison are appropriate. I use the expression data that are median ratio normalized and variance stabilizing transformed (functions in DESeq2) from the read counts to do the PAM50 classification, then I compared the results pred ...
written 7 days ago by magicpants60
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Answer: A: What kind of unit of RNA-seq should be used in machine learning models?
... I also found this post: [Difference between CPM and TPM and which one for downstream analysis?](https://bioinformatics.stackexchange.com/questions/2298/difference-between-cpm-and-tpm-and-which-one-for-downstream-analysis). The answers say TPM is better than CPM since TPM accounts for transcript len ...
written 9 days ago by magicpants60
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Comment: C: What kind of unit of RNA-seq should be used in machine learning models?
... Well I can't get your conclusion from this paper, it just says it's important to correct the selection bias and the testing data should be independent from the gene selection procedure. The problem proposed by them is due to the fact that sample sizes of datasets are often not big enough back to ear ...
written 9 days ago by magicpants60
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Comment: C: issues with GTEx data annotation files
... No problem when I open this kind of text file in Mac excel, how did you open that? Or you can just use unix command line like `cut` to extract the columns and annotate files. ...
written 6 months ago by magicpants60
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Comment: C: issues with GTEx data annotation files
... The file is tab delimited, go check your excel `Data` -> `Text to Columns` ...
written 6 months ago by magicpants60
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Answer: A: Is there a way to get the name or IDs of genes with the goseq table?
... Yes please refer to this post: https://support.bioconductor.org/p/102273/ For my own case, I modified the function # Get the gene lists of "numDFinCat" in GO.wall report getGeneLists <- function(pwf, goterms, genome, ids){ gene2cat <- getgo(rownames(pwf), genome, ids) cat ...
written 7 months ago by magicpants60
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How to interpret the eQTLs in cancer
... According to the paper [PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types][1], they conducted the eQTL mapping using RNA-seq and genotype data from TCGA. I am a bit confused about the meaning of cancer eQTL. I know that an eQTL is a locus that explains a fraction ...
tcga rna-seq snp eqtl written 7 months ago by magicpants60
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Comment: C: How To Update R In Ubuntu ?
... Update R version (3.4 -> 3.5) in Ubuntu 16.04 (xenial): sudo su echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" >> /etc/apt/sources.list apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 apt-get update apt-get install r-base ...
written 8 months ago by magicpants60

Latest awards to magicpants

Scholar 7 days ago, created an answer that has been accepted. For A: Is there a way to get the name or IDs of genes with the goseq table?
Scholar 6 months ago, created an answer that has been accepted. For A: Is there a way to get the name or IDs of genes with the goseq table?
Popular Question 15 months ago, created a question with more than 1,000 views. For Intersect vcf file and bed file

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