Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Denali
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2 hours ago
Joined:
10 years ago
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I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

<prev • 1,435 results • page 1 of 144 • next >
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Comment: C: Limma residuals matrix
... Well, I'll be. It does look like there is a `limma::residuals.MArrayLM` function defined. Try `residuals(fit, eset)` and see how it compares to `resids` above ... ...
written 2 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Limma residuals matrix
... If you're looking for the genes that are dimorphic based on sex, you've just found them. If you follow through with your "standard" limma dge pipeline, you'll get the genes differentially expressed across the sexes of your samples, ie. ``` design <- model.matrix(~Sex, data = pData(eset)) fit < ...
written 2 days ago by Steve Lianoglou ♦ 12k
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Answer: A: How can I delete specific rows (using gene name) from a DESeq2 dataset (or even
... Putting aside the rationale for wanting to remove these genes, there are many ways to do what you're after. Let's say your `DESeqDataSet` object is named `dds` and your "results table" is called `res`. Take a minute to familiarize yourself with the type of entries stored in the columns of `res`, b ...
written 2 days ago by Steve Lianoglou ♦ 12k
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Comment: C: R Version 3.6.1
... It's not clear why you have posted this. Are you having trouble installing some package and looking for help? Please modify your post to include an actual question and provide details like the command you have tried that fail, along with the error you get and the output of sessionInfo() ...
written 7 days ago by Steve Lianoglou ♦ 12k
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Comment: C: how to get normalized count data from edgeR using TMM methods
... I'm pretty sure `cpm` is all you get out of the box with edgeR. Can you elaborate on what you find insufficient about its output? Do you not like the fact that the counts are returned scaled down to "N per million", or? ...
written 9 days ago by Steve Lianoglou ♦ 12k
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Answer: A: RNA-seq normalization without filtering
... In the edgeR world, assuming you've got your data in a DGEList `y` already, you should just be able to do the following without filtering: ``` y <- calcNormFactors(y) cpms <- edgeR::cpm(y, log = TRUE) ``` Are you running into some problem doing that, or was this more of a theoretical questio ...
written 9 days ago by Steve Lianoglou ♦ 12k
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Comment: C: Mr. Anjan Payra
... Hi Anjan, if you are looking for help here, you will need to provide a lot more information on what you are trying to do and provide some context on what you already tried and why it's not satisfactory. You could, for instance, just copy and paste those gene names into [STRING][1] and hope for the ...
written 24 days ago by Steve Lianoglou ♦ 12k
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Answer: A: What can I do if I only have TPM but not raw counts data?
... It's not ideal, but your best shot will likely be to use the "limma-trend" pipeline. This question gets asked (fairly) often enough, so you can refer to some of those posts to get you started, like: 1. [Differential expression analysis starting from TPM data](https://support.bioconductor.org/p/988 ...
written 26 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Correct way to analyze the data/look at significant variations
... Regarding your filtering strategy: it looks like you are doing it backwards. That is to say, you've described your filtering strategy like so: > I am doing CPM with CPM < 5 in at least 3 samples (should I use a different method?) You want to test if the gene breaks some minimum threshold (in ...
written 4 weeks ago by Steve Lianoglou ♦ 12k
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Answer: A: "Packages required but not available." rtracklayer in OSX is not available to CR
... This is new to me. I've always been under the assumption that packages that depend/import Bioconductor packages need to be hosted by Bioconductor ("Suggests" is another story). Not that the vignette for the `remotes` package is a definitive source, but [they even conclude][1] with the following: ...
written 4 weeks ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Popular Question 7 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Popular Question 8 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
Popular Question 8 months ago, created a question with more than 1,000 views. For error in bioconductor installation
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Scholar 9 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Scholar 12 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 2.1 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 2.1 years ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: when to apply quantile normalization with voom in limma/voom framework with RNA-
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Scholar 2.3 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 3.3 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Scholar 3.3 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
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