User: Minstein

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Minstein130
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Posts by Minstein

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Can we use previous estimated ComBat model to correct batch effects for new data?
... Hi, I am puzzled about this situation: if we have estimated a ComBat model for batch effects in dataset A, can we use this model to adjust batch effect for dataset B? In another case, there are two batches, i.e., batch 1 and batch 2, in your dataset, but you just want to use 70% data of high qualit ...
batch effect microarray rna-seq batch written 9 months ago by Minstein130 • updated 9 months ago by Kevin Blighe53k
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Answer: A: Where can I find public Single Cell RNA-seq data?
... More than 20 human and mouse scRNA-seq datasets are collected by the [Hemberg Group][1]: https://hemberg-lab.github.io/scRNA.seq.datasets/ [1]: https://www.sanger.ac.uk/science/groups/hemberg-group ...
written 11 months ago by Minstein130
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Answer: A: why PCA for RNA-Seq but tSNE for scRNA-seq?
... I think tSNE is capturing **the local relationships** between points, like treating your data as a network where your cells are nodes. PCA is calculating **the "true" distances** between points after we consider **variation in your dataset**. Mahalanobis distance can do similar things. Applying PCA ...
written 14 months ago by Minstein130
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Answer: A: Unsupervised subtype discovery
... I'd say you'd better filter out some genes, because if some genes don't contribute to the subtype identification, they may add noises to your data. The assumption behind is that there should be some common features among different subtypes, but due to the measurement, there are variations in the com ...
written 14 months ago by Minstein130
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(Closed) [R/Rstudio] Can't load installed packages with "no title available" message
... I installed Rstudio in our lab's server, and run as a non-root user. I usually installed R packages in a directory created by my self and I have the privilege to read and write. However, I found packages installed previously in that directory can no longer be used, and there are error messages which ...
software error R written 14 months ago by Minstein130
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Answer: A: Merging single-cell RNA-seq from different platforms across different conditions
... Hi, Marta Two papers published this year in Nature Biotechnology solved the problem of batch effect correction between scRNA datasets: 1. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. (https://www.nature.com/articles/nbt.4091) 2. Integratin ...
written 14 months ago by Minstein130
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Comment: C: Why NMF for mutation signature analysis
... Thanks. It makes sense now. ...
written 14 months ago by Minstein130
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Comment: C: Why NMF for mutation signature analysis
... My thinking is: Sparsity can help you interpret the biological meaning for the ***metagenes***, because only a few numbers of coefficients are positive and it helps you better understand the function of that group of genes. You can think of the expression profile or mutation profile as the output of ...
written 14 months ago by Minstein130
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Answer: A: Why NMF for mutation signature analysis
... The mutational profile is naturally nonnegative. You can regard the latent k components as a combination of genes (i.e. metagene). NMF can help you see which "parts" of genes function in which class of patients. In the case of face recognition, NMF can help you identify intuitional parts of faces, ...
written 14 months ago by Minstein130
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How to predict protein domains from a list of mRNA sequences?
... I have a list of mRNA (mature mRNA) sequences. I performed the transcriptome assembly, so some of the mRNA sequences have not been annotated before. My aim is to annotate domains for all the potential amino acid sequences from these mRNAs. Some obstacles exist: - A *de novo* protein domain predic ...
genome sequence written 14 months ago by Minstein130

Latest awards to Minstein

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Why NMF for mutation signature analysis
Appreciated 7 months ago, created a post with more than 5 votes. For A: Why NMF for mutation signature analysis
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Why NMF for mutation signature analysis
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Why NMF for mutation signature analysis

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