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User: dsull

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dsull • 1.2k
Reputation:
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Location:
UCLA
Last seen:
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Joined:
3 years, 10 months ago
Email:
d****@stanford.edu

Name: Delaney Sullivan

Currently at UCLA (formerly at Stanford)

Posts by dsull

<prev • 112 results • page 1 of 12 • next >
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Answer: A: DESeq2 rlogTransformed count data have negative values. Why are they negative?
... Because it's a log transform. Taking the log of any positive number less than 1 (which some of your counts will be post-normalization) will get you a negative number. ...
written 4 days ago by dsull • 1.2k
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Answer: A: Directionality of GSEA result Vs log2FC
... I think there's some confusion. LogFC describes how an individual gene changes in expression. GSEA is for analysis of a "gene set" with respect to your expression data, not for analysis of an individual gene. ...
written 5 days ago by dsull • 1.2k
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Answer: A: Enrichr Result analysis interpretation ?
... Short answer: No, you can't use p-values to "select significant pathways"; you need to use adjusted p-values. Long answer: If you're doing hypothesis testing and want to claim "statistical significance", you should use adjusted p-values because of multiple testing. The multiple testing problem per ...
written 6 days ago by dsull • 1.2k
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Comment: C: Comparing single end and paired end TPM data
... I agree with ATpoint's assessment, especially as they plot minimum logFC (so the minimum of the logFCs obtained among the 31 comparisons) and the maximum adjusted p-value. Looking at the paper, they did a rough analysis and they probably lost statistical power to detect more candidates but that was ...
written 13 days ago by dsull • 1.2k
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Comment: C: Visualizing a set of genes in ENCODE ChIPseq dataset-Any tools or tutorials?
... You can try `deepTools` Example usage with bigwig files: https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html#usage-examples You can plot only the regions corresponding to your genes-of-interest by creating a `.bed` file and supplying it to deepTools's `computeMatrix` command ...
written 14 days ago by dsull • 1.2k
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Answer: A: Effect of sample size on log fold change in gene expression analysis
... 1. No relation; log fold change represents effect size, not uncertainty. If you remove samples, of course your log fold changes are going to change. Naively, think of a gene's fold change as the average expression of a gene in one group divided by the average expression of that gene in the other gro ...
written 14 days ago by dsull • 1.2k
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Answer: A: correct order of cut off and normalization in RNAseq data
... This is not how you do RNA-seq. You must feed your raw counts into a RNA-seq package like `DESeq2` -- it normalizes things the correct way and then you will then be able to set your cutoffs (based on log2 Fold Changes and adjusted p-values). Also, in the future, please describe your experiment in ...
written 18 days ago by dsull • 1.2k
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Comment: C: Differential Gene Expression Analysis with low biological replicates
... Based on the clustering from the plots, I can't really discern any difference between group 1 and group 2. If they were truly different, group 1 samples would mostly form one cluster while group 2 samples would mostly form another cluster. So it's probably really the case that there are no differen ...
written 19 days ago by dsull • 1.2k
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Comment: C: Searching for a specific cell type in TCGA
... You can figure out what cancers arise from which cells by looking through cancer textbooks/literature. For example, lung adenocarcinoma arises from epithelial cells, sarcomas arise from connective tissue cells, while lymphomas arise from lymphocytes. Note that, as genomax mentioned, the genomics da ...
written 19 days ago by dsull • 1.2k
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Comment: C: Differential Gene Expression Analysis with low biological replicates
... Would just like to add: 6 replicates per condition is not a low number of biological replicates. I routinely use half as many replicates per group. It's not statistically advisable to go through a ton of different workflows until you get the results you want (i.e. a good number of differentially exp ...
written 19 days ago by dsull • 1.2k

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Scholar 5 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 6 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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Scholar 6 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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