User: Gosia Nowicka

gravatar for Gosia Nowicka
Reputation:
40
Status:
New User
Location:
Basel
Last seen:
3 months ago
Joined:
3 years, 6 months ago
Email:
g****************@gmail.com

Posts by Gosia Nowicka

<prev • 5 results • page 1 of 1 • next >
1
vote
1
answer
172
views
1
answers
Answer: A: Normalized transcript/exon counts for network analysis
... Hello Maya, no, there is no way to get normalized data from the DRIMSeq workflow. This is because DRIMSeq does not need to use normalized data when comparing proportions. What you could do is to input your transcript counts into DEXSeq in the same way you did with exon counts. ...
written 4 months ago by Gosia Nowicka40
0
votes
0
answers
93
views
0
answers
Comment: C: DRIMSeq continious variable in design matrix - Error during precision estimation
... Hello Fiona, there are two different computational strategies used depending if your design is simple (multiple groups) or more complex (continuous covariates). In the fist case, DM parameters are estimated per group. In the second case, a regression approach with Hessians is used. It somehow brea ...
written 4 months ago by Gosia Nowicka40
2
votes
2
answers
240
views
2
answers
Answer: A: DEXSeq and DRIMSeq on paired samples?
... In DRIMSeq, based on the design matrix, you would set the full model as design_full <- model.matrix(~ cond + pair, data = samples(d)) and use it in dmPrecision() and dmFit(). In dmTest(), you can specify which coefficient you would like to test with coef = "condpre" or coef = "condpost", depen ...
written 9 months ago by Gosia Nowicka40
0
votes
1
answer
275
views
1
answers
Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... Hello Fiona, I am very sorry for my late reply. You have mentioned that the design matrix from DRIMSeq output is different than what you feed in. Would you like that I have a look on that? If yes, would share with me the d object after running the analysis? You could send it to gosia.nowicka@uzh.ch ...
written 11 months ago by Gosia Nowicka40
1
vote
1
answer
579
views
1
answers
Answer: A: Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
... Dear Kristoffer,  I am glad you find DRIMSeq useful.  I have been working on implementing the isoform-level analysis which are based on the beta-binomial distribution.  Additionally, there will be a full regression framework available for gene-level and feature-level analysis allowing for modelin ...
written 2.5 years ago by Gosia Nowicka40

Latest awards to Gosia Nowicka

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour