User: mike-zx

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mike-zx230
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Posts by mike-zx

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Documentation on the contents of the "pubtatordb" package in R?
... Pubtator is a text-mining tool which can be used to check for reported relationships between genes in literature (papers) among other useful things. The authors have several publications including a recent 2019 one. There is also an R [package][1] called `pubtatordb` which is handy as it setups a lo ...
pubtator R written 14 days ago by mike-zx230
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Comment: C: Interpretation of "standardized expression matrix"?
... but if for some analysis you wanted to do PCA with the samples as the features, would it be ok to do the z-score transformation row-wise (genes) and then again over the columns (samples) right before PCA? For example, some correction techniques have been tested for coexpression analysis in which yo ...
written 6 months ago by mike-zx230
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Comment: C: Interpretation of "standardized expression matrix"?
... Maybe I'm getting confused and scaling for PCA is just something done as part of the procedure and standardizing for expression matrices is something unrelated... ...
written 6 months ago by mike-zx230
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Comment: C: Interpretation of "standardized expression matrix"?
... Thank you once again for your answers Kevin, what still confuses me is that PCA does the transform column wise while the example you mentioned of scRNA-seq would do it row wise to transform each gene across all cells. Is it the same doing transform column or row wise? I would say no intuitively, bu ...
written 6 months ago by mike-zx230
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Interpretation of "standardized expression matrix"?
... I've seen the term been used in some papers working with gene expression data. I assume they refer to performing z-score normalization on the expression matrix, but I would like to know if this is the right interpretation. Also, is this typically done over each gene vector (rows of a traditional exp ...
normalization rna-seq written 6 months ago by mike-zx230 • updated 6 months ago by Kevin Blighe68k
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How to interpret "pseudo count" in gene expression data handling context?
... I am reading a paper that has a passage describing the pre-processing of gene expression data before conducting the experiments. The passage states "After conversion to a base-2 logarithm with a pseudo count of 0.125, batch normalization using ComBat was applied". What exactly is a pseudo count? Wh ...
normalization rna-seq written 7 months ago by mike-zx230 • updated 7 months ago by ATpoint42k
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Comment: C: Error using the getGEO() patcher
... Tried it on a macOS system without trouble, weird that it just doesn't work in the windows machine. ...
written 8 months ago by mike-zx230
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Comment: C: Error using the getGEO() patcher
... I successfully installed with `devtools::install_github("https://github.com/seandavi/GEOquery")`. The version is now 2.55 as shown in the session info, however the same exact problem in the original post persists. R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Ru ...
written 8 months ago by mike-zx230
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Comment: C: Error using the getGEO() patcher
... yes, I do have the appropriate permissions. For some reason I can't get the 2.54 version of the package by updating bioconductor. ...
written 8 months ago by mike-zx230
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Error using the getGEO() patcher
... I'm trying to fetch files using the `getGEO()` function from the `GEOQuery` package in R. Upon loading the package and trying, I get a known error which can be solved via a patcher function as described in this post: [https://www.biostars.org/p/294606/][1] However, after following the steps to solv ...
R bioconductor geoquery written 8 months ago by mike-zx230 • updated 6 months ago by Biostar ♦♦ 20

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