User: I.Castanho

gravatar for I.Castanho
I.Castanho50
Reputation:
50
Status:
New User
Location:
Last seen:
3 months, 3 weeks ago
Joined:
1 year, 7 months ago
Email:
I*********@exeter.ac.uk

Posts by I.Castanho

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answers
190
views
1
answers
Comment: C: Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for sl
... I also tried updating DESeq2 and running everything again, but the errors persist. ...
written 4 months ago by I.Castanho50
0
votes
1
answers
190
views
1
answers
Comment: C: Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for sl
... Is there any way I could solve this now, without having to run everything again? > dds <- updateObject(dds) Error in validObject(result) :   invalid class “DESeqDataSet” object: undefined class for slot "rowRanges" ("GenomicRangesORGRangesList")   ...
written 4 months ago by I.Castanho50
0
votes
1
answers
190
views
1
answers
Comment: C: Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for sl
... Hi Michael,   Thank you  for replying so promptly. I was actually wondering if it had anything to do with possible system updates. I forgot to save the version of bioconductor from when I previously ran DESeq2, but DESeq2 version is the same. Details for the current sessionInfo() below.   R vers ...
written 4 months ago by I.Castanho50
0
votes
1
answer
190
views
1
answer
Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for slot rowRanges GenomicRangesORGRangesList
... Hi, I am getting a new error with DESeq2 and I have no idea why as these are commands I have run a million times. I really can't understand why it's not working anymore and I can't find any post of someone reporting this error before. I have this object: I am getting a new error with DESeq2 and I ...
deseq2 plotcounts rowranges written 4 months ago by I.Castanho50 • updated 4 months ago by Michael Love20k
0
votes
1
answers
2.3k
views
1
answers
Comment: C: DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
... Right! To be honest I didn't quite understand the listValues argument when writing that part, but it makes sense now! Thank you. Yes, and yes -- that's exactly what I want: genes which vary over time (i.e. with aging), and genes that show a different expression profile over time when comparing the ...
written 19 months ago by I.Castanho50
0
votes
1
answers
8.7k
views
1
answers
Comment: C: DESEq2 comparison with mulitple cell types under 2 conditions
... Done. Thank you! ...
written 19 months ago by I.Castanho50
7
votes
1
answer
2.3k
views
14 follow
1
answer
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
... Hello, I have a similar experiment to this one: Design formula and Design matrix in DESeq This one might be useful to compare with as well: DESEq2 comparison with mulitple cell types under 2 conditions   I have 2 groups for genotype (Mut vs. Ctr), and 4 time points, with 8 biological replicates ea ...
rnaseq deseq2 design lrt reduced model written 19 months ago by I.Castanho50 • updated 9 days ago by evocanres0
0
votes
1
answers
8.7k
views
1
answers
Comment: C: DESEq2 comparison with mulitple cell types under 2 conditions
... Dear Michael, I have a similar experiment to this one: https://support.bioconductor.org/p/67655/ I have 2 groups for genotype (Mut vs. Ctr), and 4 time points, with 8 biological replicates each. As I am interested in the interactions, I ran my model as you suggested in the manual and in similar po ...
written 19 months ago by I.Castanho50

Latest awards to I.Castanho

Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
Student 19 months ago, asked a question with at least 3 up-votes. For DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 231 users visited in the last hour