User: mat.lesche

gravatar for mat.lesche
mat.lesche10
Reputation:
10
Status:
New User
Location:
Germany
Last seen:
1 day, 2 hours ago
Joined:
2 years, 4 months ago
Email:
m*********@gmail.com

Posts by mat.lesche

<prev • 35 results • page 1 of 4 • next >
0
votes
1
answers
60
views
1
answers
Answer: A: dexseq doesn't identify exons as differential
... Hi Assa, DEXSeq doesn't look for differential expression. The tool is designed to look for a differential usage of single exon bins compared to the usage of all other exon bins in a gene. In your case the gene shows an over expression in EB2 compared to the other condition. Hence the high expressio ...
written 6 days ago by mat.lesche10
0
votes
0
answers
44
views
0
answers
counting with htseq script in DEXSeq
... Hey, I'm using DEXSeq on my data for a differential exon usage analysis. My data is paired-end data with the R1 read being on same strand as genomic feature and the R2 read is on the opposite strand. Therefore I set the right setting in the dexseq_count script and set paired = yes as well. I ran th ...
dexseq_count htseq dexseq written 7 days ago by mat.lesche10
0
votes
1
answers
138
views
1
answers
Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Thanks for your answer, I really appreciate your help! Because we have another project with 10 comparisons coming up, I'd really like to know at how many comparisons one should do the global corrections? Sorry for all the questions but I always learn something new here. ...
written 4 months ago by mat.lesche10
0
votes
1
answers
138
views
1
answers
Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Hey Michael, Thanks for mentioning the global corrections. I wasn't aware of it. Maybe it would be helpful to add this to the Q&A of the DESeq2 vignette and to refer to the section in the limma vignette? For how many pairwise comparisons do you recommend to do the global corrections? Should one ...
written 4 months ago by mat.lesche10
0
votes
1
answers
138
views
1
answers
Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Hey Michael, I did the PCA again without the sex chromosomes and PC1 went from 50 to 55% and PC2 from 26 to 23%. A plot of genes with the highest variance doesn't show Xist anymore. So I stick to ~sex+group and that's all I can do. ...
written 4 months ago by mat.lesche10
0
votes
1
answers
138
views
1
answers
Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Dear Michael, Thanks for the answer and the confirmation. I have found this thread in which you answered a question regarding pairwise comparison (https://support.bioconductor.org/p/87671/) Does your answer apply to my task as well. I have 28 comparisons because I have 8 pairs. Thanks Mathias ...
written 4 months ago by mat.lesche10
0
votes
1
answers
138
views
1
answers
Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Hey Ryan, Sorry this was my mistake and was not precise. It's not a cell line, it's two different mouse line. One is our standard mouse line, the other one is infected with a disease. ...
written 5 months ago by mat.lesche10
0
votes
1
answer
138
views
1
answer
Grouping a multifactor design in DESeq2 and accouting for sex
... Hello, I want to do an analysis of some mice data with DESeq2. We have a total 24 samples and three factors. Factor one is the genotyp (6 wildtype, 6x knockout 1, 6x knockout2, 6x knockout3) and factor two are two different cell lines (cellA and cellB). Factor three is the sex (male and female ...
deseq2 group multiple factor design written 5 months ago by mat.lesche10 • updated 5 months ago by Michael Love11k
0
votes
1
answers
726
views
1
answers
Comment: C: junction.bed to GTF to use in DEXSeq
... Hello Rahel, there is a new tool which looks and differential usage for exons and junction loci. I'm testing it at them moment because I never finished working on my version. Have a look: http://hartleys.github.io/JunctionSeq/ ...
written 14 months ago by mat.lesche10
0
votes
1
answers
726
views
1
answers
Comment: C: junction.bed to GTF to use in DEXSeq
... hey rahel, my apologies for the late reply and I have to say, that I didn't proceed. I had to stop working on this and have to focus on something else. But I hope I can get back to it soon. Mathias ...
written 17 months ago by mat.lesche10

Latest awards to mat.lesche

Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 14 months ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 14 months ago, created a question with more than 1,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 248 users visited in the last hour