User: Catalina Aguilar Hurtado

Reputation:
50
Status:
Trusted
Location:
United States
Last seen:
1 day, 6 hours ago
Joined:
3 years, 9 months ago
Email:
c******@gmail.com

Postdoc at the Cooperative Institute for Marine and Atmospheric Studies (CIMAS)

Posts by Catalina Aguilar Hurtado

<prev • 39 results • page 1 of 4 • next >
0
votes
1
answers
166
views
1
answers
Comment: C: DESeq2 interaction term
... That is good know. I was getting just a few diff. expressed genes for that genotype and wasn't sure if it was because I don't have a replicate sample.  ...
written 1 day ago by Catalina Aguilar Hurtado50
0
votes
1
answers
166
views
1
answers
Comment: C: DESeq2 interaction term
... Hi Michael, just a quick question. I have 1 genotype that doesn't have a biological replicate (1 sample in control and 1 in treatment). Should I discard it when getting the effects of each genotype to the treatment? Thanks again ...
written 2 days ago by Catalina Aguilar Hurtado50
0
votes
1
answers
166
views
1
answers
Comment: C: DESeq2 interaction term
... Thanks Michael! Just to check when I write as below, I get treatment effect for genoA without reference level results <-results(dds, name="genoA.condT1") Then compare the pairs genoA vs genoB:  results <-results(dds, contrast=list(c("genoA.condT1","genoB.condT1"))) ...
written 4 days ago by Catalina Aguilar Hurtado50
0
votes
1
answers
166
views
1
answers
Comment: C: DESeq2 interaction term
... When I refer to the others I mean geno A vs geno C and so on. Then I should use: design(dds) <- ~ geno + cond + geno:cond But this will always refer to a reference level when I want to effect of genotype X? it would compare genotype X to reference genotype? I will try to plots as well, thanks. ...
written 8 days ago by Catalina Aguilar Hurtado50 • updated 8 days ago by Michael Love16k
0
votes
1
answers
166
views
1
answers
Comment: C: DESeq2 interaction term
... Sorry Michael, I didn't explain properly. Not the effect of genotype 1 in particular, just the effects of any of the genotypes to the treatment. First I want to know what is the response of genotype X to the treatment. Second it would be interesting to know how genotypes X compares with the others i ...
written 9 days ago by Catalina Aguilar Hurtado50
0
votes
1
answers
166
views
1
answers
Comment: A: DESeq2 interaction term
... Thanks Michael. If I may as you further.  I want to get the effect of my treatment to 1 genotype to then compare with the others. I have 2 conditions (Co1 and T1) and 5 genotypes. It seems to me from the manual that I should be getting the results per gene per condition (IIIB and IIIA) while I am ...
written 9 days ago by Catalina Aguilar Hurtado50
0
votes
1
answer
166
views
1
answer
DESeq2 interaction term
... Hi, I have samples from 5 genotypes and 2 conditions. I am reading the 'Extract results from a DESeq analysis'   dds$genotype <- factor(rep(rep(c("I","II","III"),each=3),2)). But do not understand the 'each=3),2)' in this line, as I need to modify it for my 5 genotypes. Also, I am interested ...
deseq2 written 9 days ago by Catalina Aguilar Hurtado50
0
votes
1
answers
86
views
1
answers
Comment: C: Deseq2 raw counts input as integers
... Thanks Michael. I was not sure if it was ok to round the counts.  ...
written 11 days ago by Catalina Aguilar Hurtado50
0
votes
1
answer
86
views
1
answer
Deseq2 raw counts input as integers
... Hi, I generated a 'RSEM.gene.counts.matrix' which are the raw counts from a Trinity 'abundance_estimates_to_matrix.pl' script. However, these counts are not integers, is there a way I could use this matrix in Deseq2 or I will have to generate it again using a method from the Deseq2 manual? Thanks, ...
deseq2 written 11 days ago by Catalina Aguilar Hurtado50 • updated 11 days ago by Michael Love16k
0
votes
1
answer
266
views
1
answer
Genotypic difference design using deseq2
... Hi I am currently working on my experimental design and would like to use DESeq2 to analyze my data.  For this experiment I would like to understand the differences among genotypes under a treatment.  I have 5 genotypes and would like your advice on the minimum number of biological replicates. Can ...
deseq2 experimental design genotype written 12 months ago by Catalina Aguilar Hurtado50 • updated 12 months ago by Michael Love16k

Latest awards to Catalina Aguilar Hurtado

Popular Question 22 months ago, created a question with more than 1,000 views. For DESeq vs DESeq2 have different DEGs results
Popular Question 22 months ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Popular Question 22 months ago, created a question with more than 1,000 views. For Report and compare log2FC vs FC
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 180 users visited in the last hour