User: darklings

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darklings70
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Posts by darklings

<prev • 25 results • page 1 of 3 • next >
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Comment: C: How to interpret the eQTLs in cancer
... Oh wow thanks, now I am a bit confused about why I asked this question at that time... ...
written 3 days ago by darklings70
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... should be the `cpm()` function? ...
written 4 months ago by darklings70
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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 4 months ago by darklings70
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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 4 months ago by darklings70
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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 4 months ago by darklings70
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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 4 months ago by darklings70
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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 11 months ago by darklings70
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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 11 months ago by darklings70
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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 11 months ago by darklings70
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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 11 months ago by darklings70 • updated 7 days ago by cao5109270

Latest awards to darklings

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Is there a way to get the name or IDs of genes with the goseq table?
Scholar 4 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?
Scholar 11 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 19 months ago, created a question with more than 1,000 views. For Intersect vcf file and bed file

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