User: mike-zx

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mike-zx190
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Posts by mike-zx

<prev • 46 results • page 1 of 5 • next >
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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 1 day ago by mike-zx190
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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 2 days ago by mike-zx190
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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 2 days ago by mike-zx190
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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 2 days ago by mike-zx190 • updated 2 days ago by zx87549.1k
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Answer: A: Correlation vs differential expression testing
... It all depends on what the intent of your project is. Differential Expression Analysis will tell you if certain genes are notably expressed in some of your samples relative to all samples. If you do correlation between samples, the information you are getting isn't quite the same; with correlation b ...
written 5 weeks ago by mike-zx190
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What are some references of works that use a TPM expression threshold for filtering samples/genes?
... I'm struggling to find papers that use transcripts per million (TPMs) on their pre-processing steps for filtering out non-expressed genes or very low expression genes. I'm aware that filtering is usually recommended with raw read counts as they provide more information to work with for the decision, ...
rna-seq written 6 weeks ago by mike-zx190 • updated 27 days ago by Biostar ♦♦ 20
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Extra adjustment variables during batch effect correction
... I've been looking into ComBat lately for batch effect correction of my expression data and I've become curious of one of the features of the R implementation of the SVA package. According to the [tutorial][1], when using ComBat one must obviously provide the expression matrix to correct and the batc ...
combat rna-seq batch effect correction written 11 weeks ago by mike-zx190
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Comment: C: statistics method to find the relation between multiple variables of 50 samples
... what exactly are these variables? maybe gene expression? ...
written 11 weeks ago by mike-zx190
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Comment: C: Can I use batch effect correction "by parts"?
... yeah I will consult for options with my colleagues, I will have access to a 16 RAM PC in February, but that would mean delaying work. ...
written 12 weeks ago by mike-zx190
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Comment: C: Can I use batch effect correction "by parts"?
... that sounds reasonable, however taking a look at the paper again I notice in step one of the algorithm (standardize data) that maybe the full matrix of genes is expected. (talking about this [paper][1]) [1]: https://academic.oup.com/biostatistics/article/8/1/118/252073 ...
written 12 weeks ago by mike-zx190

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Scholar 5 weeks ago, created an answer that has been accepted. For A: manipulating a file by R or bash?
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