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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Answer: A: How to extract the voom normalized value for each observation?
... I doubt you can combine these into a single number in any meaningful way. You need an algorithm that can take observations and their weights and use them productively together ... ...
written 6 months ago by Steve Lianoglou12k
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Comment: C: Tac and Bioconductor giving different results
... You are likely right, you shouldn't be seeing such large differences. Again, no one can help you because we can't debug stories -- you need to provide code. You probably want to RMA normalize your data and use limma for analysis. You hopefully have some intuition of the experiment you are analyzing ...
written 7 months ago by Steve Lianoglou12k
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Answer: A: Tac and Bioconductor giving different results
... This is an impossible question to answer. Although I (and likely most people here) have never used "TAC affymetrix software" (I guess you mean this?), I imagine there are a multitude of ways to perform an analysis there just as there are many ways to perform an analysis using various bioconductor t ...
written 7 months ago by Steve Lianoglou12k
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Answer: A: Best DEG tool for datasets with FPKM counts?
... For analysis, you will want to log2 transform the fpkm values and use the limma-trend pipeline, see here: https://support.bioconductor.org/p/56275/ As for the gene_id column, you're only looking in the land of "funny looking" gene ids. Take a random sampling of the gene_id values, ie. if you have ...
written 7 months ago by Steve Lianoglou12k
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Comment: C: edgeR cpm filter
... Everything is working as it should and, further, your filtering strategy should be blind to the groups each sample belongs to. You can either increase your filtering threshold (ie. keep <- rowSums(cpm(y) > 2) >=5) if you want to remove more (any) genes, or you can switch to filtering based ...
written 8 months ago by Steve Lianoglou12k
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Comment: C: edgeR cpm filter
... The code itself looks like it should work, so when you say "this doesn't work", what do you mean, exactly? Are you getting an error somewhere, or? Also, if you have 6 replicates per group your keep rowSums threshold should technically be >= 6, but this probably won't change much in the downstrea ...
written 8 months ago by Steve Lianoglou12k
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Answer: A: Add new columns to DESeqResults from text file by matching rownames.
... Call as.data.frame on your DESqResults objects before the merge, ie. out <- merge(as.data.frame(result.ASE_Data), geneMap, ...) merge doesn't match by rownames, though, so you will have to specify the correct value for by, or a by.x and by.y combination of the column names in your result.ASE_D ...
written 8 months ago by Steve Lianoglou12k
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Comment: C: Differential expression of nomalised and log2 transformed data in limma
... Your design matrix is constructed from a factor (vector) that is 100 elements long. The first 50 are "1" and the second "50" are "2", but you said yourself that you have 25 elements per group, so ... why are you doing rep(..., each=50)? Fix it so that you have as many labels as samples ... and, btw ...
written 9 months ago by Steve Lianoglou12k
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Answer: A: DESeq2 Which gene used to normalize?
... Unless you specify a set of control genes to use, every gene which has all-non-zero-observations is used. See the help in ?estimateSizeFactors and ?estimateSizeFactorsForMatrix for more information. ...
written 9 months ago by Steve Lianoglou12k
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Answer: A: Expression profile from $E from Voom
... 1) expression profile in Elist has performed log(CPM) and been normalized for library size, right? Yes 2) Has the expression profile in Elist incorporated the precision weights (represented as $weights in v object) yet? No Note that if you want to use the expression data in your voomed "v" objec ...
written 9 months ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Good Answer 12 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 12 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 12 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 12 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Scholar 12 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 13 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Scholar 2.2 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 2.2 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 2.2 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Scholar 2.2 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.3 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 2.4 years ago, received more than 100 upvotes.
Scholar 2.4 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.7 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest

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