Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Denali
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I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

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Comment: C: scRNA-seq: a question about the names of the columns in a Seurat object
... I would advise you to reference the relevant literature ;-) The MNN paper does a comparison against COMBAT and shows their method to be superior, and the Seurat preprint claims their method to be superior to MNN. If it were me, I'd likely ignore COMBAT and take my time with MNN, LIGER, and Seurat ...
written 2 days ago by Steve Lianoglou ♦ 12k
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Answer: A: scRNA-seq: a question about the names of the columns in a Seurat object
... For better or for worse, Seurat isn't a Bioconductor package, so this board is technically not the right/best place to get help on using it. That having been said: You are likely seeing the <ExperimentN>_<barcodeY> column names because the same barcodes are used across samples/expe ...
written 2 days ago by Steve Lianoglou ♦ 12k
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Comment: C: DESeq2: Small treatment group, large control group
... Searching through google with a site:support.bioconductor.org modifier(?) is almost always better than using the search functionality baked into this board. For instance, googling for: unbalanced groups rnaseq site:support.bioconductor.org gets you a few hits: https://support.bioconductor.org/p/9 ...
written 4 days ago by Steve Lianoglou ♦ 12k
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Comment: C: Fisher test in Rna seq
... I'll echo what Anna said, but with more conviction: you absolutely should not use a fisher.test for this. Use edgeR, limma/voom, or DESeq2. ...
written 4 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Help for Research Proposal
... I'm not quite sure what forum to direct you to so that you can get the best help for this question, but honestly this one isn't it. That having been said, it's hard for me not to try to offer some help, so just a few thoughts: I'd first go back to have a chat with your supervisor and see if sh ...
written 10 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Get normalized COUNTS Deseq2
... You need to call counts() on your DESeqDataSet object. This is the object that stores your count data. You are currently calling counts() and the object you received from calling results(...) on your DESeqDataSet object. This results object merely holdes the statistics for a particular contrast of i ...
written 10 days ago by Steve Lianoglou ♦ 12k
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Comment: C: Data normalization and transformation using DESeq2
... Yes, you should. But if you haven't done that already, the rlog function will do that internally. ...
written 11 days ago by Steve Lianoglou ♦ 12k
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Answer: A: DESeq2 namespace load fail
... The "namespace ‘htmlTable’ 1.7 is being loaded, but >= 1.11.0 is required" error tells you that your version of the htmlTable package is too old. You have version 1.7 but DESeq2 requires that you use at least 1.11.0 You can verify this by looking at the output of packageVersion("htmlTable") As ...
written 29 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Seurat to SingleCellExperiment Converting error in MAC
... I'm pretty sure you are getting the "'x' must be an array of at least two dimensions" error in this code block: keep_feature <- rowSums(counts(sce) > 0) > 0 Because the counts function is returning a sparse matrix, and you are using the base::rowSums function, which doesn't know how to h ...
written 5 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: Finding DE genes from RNA-seq data
... Hi Maryam, In short: no, I really can't. It sounds like you are at the early stages of a long journey on a project that needs a lot of care (wether it's worth while, I'll leave that up to you to decide :-) If you are asking me how to transform RNA-seq data so that it is "best used" as features for ...
written 5 weeks ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Scholar 6 weeks ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 6 weeks 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 4 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 4 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?
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 17 months 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 17 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 17 months 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 17 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 17 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Scholar 19 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Scholar 2.6 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Scholar 2.6 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 2.6 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 2.6 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.8 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
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