User: darklings

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darklings90
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Posts by darklings

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Is there a way to get the name or IDs of genes with the goseq table?
... I am not sure, maybe `getgo()` doesn't support your genome. Could you provide a bit more details about your species and code/error? ...
written 7 months ago by darklings90
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Comment: C: Getting information about shortening or lengthening of UTRs from RNAseq data
... Some other tools first identify de novo APA sites from RNA-seq and then test which genes have shortening or lengthening UTRs. I tried QAPA and another labmate tried DaPars, and the results are quite different... ...
written 8 months ago by darklings90
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Comment: C: output TMM normalized counts with edgeR
... Hi, I am wondering why the `estimateTagwiseDisp()` is needed? Does it change anything for the output? ...
written 8 months ago by darklings90
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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 9 months ago by darklings90
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... should be the `cpm()` function? ...
written 14 months ago by darklings90
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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 14 months ago by darklings90
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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 14 months ago by darklings90
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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 14 months ago by darklings90
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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 14 months ago by darklings90
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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 20 months ago by darklings90

Latest awards to darklings

Popular Question 5 months ago, created a question with more than 1,000 views. For How to analyze the variants in non-coding regions
Popular Question 5 months ago, created a question with more than 1,000 views. For What cause the differences between genes annotations from different databases?
Popular Question 5 months ago, created a question with more than 1,000 views. For What kind of unit of RNA-seq should be used in machine learning models?
Supporter 6 months ago, voted at least 25 times.
Teacher 11 months 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 14 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 20 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 2.4 years ago, created a question with more than 1,000 views. For Intersect vcf file and bed file

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