Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
12,030
Status:
Trusted
Location:
Denali
Scholar ID:
Google Scholar Page
Last seen:
7 hours ago
Joined:
9 years, 1 month 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 • 1,387 results • page 2 of 139 • next >
0
votes
1
answers
237
views
1
answers
Answer: A: featureCounts taking 4-10 hours per BAM file?
... Somethings you might want to think about: How much RAM do you have?; and Is your external HD to blame? Does it go any faster if you move it to your local HD? (hopefully an SSD :-) ...
written 5 months ago by Steve Lianoglou12k
0
votes
1
answers
213
views
1
answers
Answer: A: Can Tximport average transcript length be used for GOSeq?
... Yes it can, and it's arguably a better value to use than what is in the database anyway. ...
written 6 months ago by Steve Lianoglou12k
0
votes
2
answers
1.5k
views
2
answers
Comment: C: Installing an older release of Bioconductor
... This may *technically* work, however the bioconductor ecosystem (v3.4, v3.5, etc) is only tested to work against a very specific version of R. Installing bioc packages using anything but `biocLite()` can land you into a mess. It doesn't mean that you can't try, but you'll be on your own if/when thin ...
written 6 months ago by Steve Lianoglou12k
0
votes
2
answers
321
views
2
answers
Answer: A: Incredibly high/low foldChange
... A 39e6 fold change seems crazy ... but, of course, if a gene has all zero counts in one group, and some counts in another than the fold change is infinite, right? Whatever the case may be, it does warrant further inquiry. This first thing you should do is try to visualize your data. DESeq2 has a " ...
written 6 months ago by Steve Lianoglou12k
0
votes
3
answers
225
views
3
answers
Answer: A: voom command broken in limma_3.34.5?
... The Error in round(counts) : non-numeric argument to mathematical function you are getting suggests that your counts object isn't what you think it is. What is the output of class(counts) and class(counts[1])? ...
written 8 months ago by Steve Lianoglou12k
0
votes
1
answers
452
views
1
answers
Comment: C: Limma RNA seq analysis_VOOM
... It's not stored anywhere in the sense that you are thinking. These covariates are just accounted for inside the linear model. If you want to explore what your data looks like when these covariates are accounted for, take a look at limma's removeBatchEffects function. ...
written 8 months ago by Steve Lianoglou12k
0
votes
1
answers
286
views
1
answers
Answer: A: Does bioconductor now has microarray cross-platform merging and normalization me
... You haven't said what you would want to do the cross-platform merging for, but I think you're going down the wrong rabbit hole. Often times people inquire about merging different platforms so that they can combine different studies that are about "the same thing" and increase their N. If this is wh ...
written 9 months ago by Steve Lianoglou12k
0
votes
1
answers
380
views
1
answers
Comment: C: Unbalanced experiment with multiple samples from each patient.
... Great answer, as usual, but I think the OP should pay particular attention to the "assuming they are technical replicates" bit of this answer. It might be useful for the OP to elaborate on how repeated "healthy" or "diseased" measures from the same patient are ending up in these data. For instance, ...
written 9 months ago by Steve Lianoglou12k
0
votes
2
answers
424
views
2
answers
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 9 months ago by Steve Lianoglou12k
0
votes
1
answers
269
views
1
answers
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 10 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 15 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 15 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 15 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 15 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 15 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 16 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.4 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 2.4 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 2.4 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Scholar 2.4 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.6 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 2.6 years ago, received more than 100 upvotes.
Scholar 2.6 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 182 users visited in the last hour