Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
12,110
Status:
Trusted
Location:
Denali
Scholar ID:
Google Scholar Page
Last seen:
1 day, 11 hours ago
Joined:
9 years, 4 months ago
Email:
s*********@gmail.com

I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

<prev • 1,401 results • page 2 of 141 • next >
0
votes
1
answers
93
views
1
answers
Answer: A: TMM normalization of cancer RNA seq
... You are getting negative values because you are calling cpm(...) with log = TRUE. Some of your raw/unlogged counts-per-million values are falling between 0 and 1, and therefore their log2 values are negative. ...
written 5 weeks ago by Steve Lianoglou12k
0
votes
2
answers
158
views
2
answers
Answer: A: Finding DE genes from RNA-seq data
... To supplement/complement Ryan's rather thorough answer, I think it'd still be useful if you read through this edgeR/quasi-likelihood workflow, in case you haven't seen it yet: From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi ...
written 7 weeks ago by Steve Lianoglou12k
0
votes
0
answers
114
views
0
answers
Comment: C: Newbie to all of this
... And perhaps tell us a bit more about the types of data and analyses you are being asked to support ...
written 8 weeks ago by Steve Lianoglou12k
0
votes
1
answers
88
views
1
answers
Answer: A: Normalization and Quality Control for Multiple scRNAseq Data Sets
... There is a great series of articles written by Aaron Lun, Davis McCarthy, and John Marioni that outline various aspects of working with single cell data in the bioconductor-verse, I will link to both the "release" and "development" version of these articles. If I were you I'd focus on the devel stu ...
written 9 weeks ago by Steve Lianoglou12k
0
votes
1
answers
170
views
1
answers
Comment: C: EdgeR vs DESeq2 with/without lfcShrink
... Did someone call?    ...
written 3 months ago by Steve Lianoglou12k
0
votes
2
answers
244
views
2
answers
Comment: C: CQN offset and edgeR
... From your two results, out of the five genes you are showing, I see three genes whose logFC's have changed slightly, and two genes that are completely different in their identity. ...
written 3 months ago by Steve Lianoglou12k
0
votes
2
answers
244
views
2
answers
Comment: C: CQN offset and edgeR
... Sure, why don't you try to scramble the values in your cqn offset matrix and see if those don't look any different. This is untested, but I think should work: y2 <- y y2$offset <- matrix(sample(y$offset), nrow = nrow(y$offset)) # ... redo the edgeR steps and test the same contrast Also, how ...
written 3 months ago by Steve Lianoglou12k
0
votes
2
answers
244
views
2
answers
Answer: A: CQN offset and edgeR
... You can make your life a bit easier by following the code provided in the cqn vignette a bit more closely. There you'll see that the cqn glm.offset matrix is added to the DGEList directly So, modifying your code a bit and using Gordon's suggest contrast: mycqn <- cqn(countData,lengths=uCovar$Gen ...
written 3 months ago by Steve Lianoglou12k
0
votes
1
answers
155
views
1
answers
Answer: A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
... Here are some options: Get the data from this paper, where the reprocessed the TCGA RNA-seq data using subread (GEO link). The recount project has a reprocessed version of the TCGA data. Click on the TCGA tab at the top there. The ARCHS4 project provides the "recount"ed TCGA data as and HDF5 fi ...
written 4 months ago by Steve Lianoglou12k
0
votes
3
answers
176
views
3
answers
Answer: A: Difficulty extending ExpressionSet
... The RccSet class in the NanoStringQCPro package extends ExpressionSet, and I don't really see any wholesale copying of any code in there at all. ...
written 4 months ago by Steve Lianoglou12k

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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 144 users visited in the last hour