User: dsull

gravatar for dsull
dsull1.2k
Reputation:
1,240
Status:
Trusted
Location:
UCLA
Last seen:
an hour ago
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 >
3
votes
1
answer
99
views
1
answers
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 dsull1.2k
0
votes
1
answer
66
views
1
answers
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 dsull1.2k
0
votes
1
answer
70
views
1
answers
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 dsull1.2k
0
votes
1
answer
122
views
1
answers
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 dsull1.2k
0
votes
0
answers
99
views
0
answers
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 dsull1.2k
3
votes
1
answer
82
views
1
answers
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 dsull1.2k
1
vote
1
answer
69
views
1
answers
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 dsull1.2k
0
votes
0
answers
119
views
0
answers
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 dsull1.2k
0
votes
0
answers
66
views
0
answers
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 dsull1.2k
1
vote
0
answers
119
views
0
answers
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 dsull1.2k

Latest awards to dsull

Scholar 4 days ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Supporter 13 days ago, voted at least 25 times.
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 28 days ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Centurion 28 days ago, created 100 posts.
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Guru 8 weeks ago, received more than 100 upvotes.
Scholar 8 weeks ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Scholar 3 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Why could we infer a physical time scale (e.g. a billion year) from a phylogenet
Scholar 4 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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 5 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
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
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
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
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Why could we infer a physical time scale (e.g. a billion year) from a phylogenet
Scholar 6 months ago, created an answer that has been accepted. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 803 users visited in the last hour