User: Catalina Aguilar Hurtado

Reputation:
50
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Trusted
Location:
United States
Last seen:
3 months, 1 week ago
Joined:
4 years, 10 months ago
Email:
c******@gmail.com

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

Posts by Catalina Aguilar Hurtado

<prev • 43 results • page 1 of 5 • next >
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Comment: C: edger glmQLFit mix glmLRT
... Ryan and Aaron thanks so much for your detailed explanation. I understand now what happen to my data and good to know it is wrong to mix them (even by mistake). I know getting more DEGs doesn't mean that the analysis is good, just with poorly annotated organism can be hard to answers the biological ...
written 12 months ago by Catalina Aguilar Hurtado50
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edger glmQLFit mix glmLRT
... Hi sorry for the random question. I was using edger and used:  "fit <- glmQLFit(y, design) " followed by: "lrt <- glmLRT(fit, coef=6) " instead of using glmQLFTest  and got some interesting results. Which of course changed to very few degs when saw the mistake and I used the actual  glmQLFTest ...
edger written 12 months ago by Catalina Aguilar Hurtado50 • updated 12 months ago by Aaron Lun23k
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Comment: C: DESeq2 interaction term
... Thanks, I see what you mean. Now that I checked all the genotypes I get 1 genotype with less DEG when it is run on its own, which seems be the one with more variability (also strongest physiological response to treatment). I am now thinking if it would be accepted to present results from different m ...
written 12 months ago by Catalina Aguilar Hurtado50
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Comment: C: DESeq2 interaction term
... Hi Michael, I was reading the manual about running a group of samples together or by pairs. I am getting more diff. expressed genes when I ran e.g. genotype A on its own (~condition) than with the other genotypes (~ geno + geno:condition). The genes in common between the two designs have very simila ...
written 12 months ago by Catalina Aguilar Hurtado50
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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 12 months ago by Catalina Aguilar Hurtado50
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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 12 months ago by Catalina Aguilar Hurtado50
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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 13 months ago by Catalina Aguilar Hurtado50
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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 13 months ago by Catalina Aguilar Hurtado50 • updated 13 months ago by Michael Love22k
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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 13 months ago by Catalina Aguilar Hurtado50
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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 13 months ago by Catalina Aguilar Hurtado50

Latest awards to Catalina Aguilar Hurtado

Popular Question 3 months ago, created a question with more than 1,000 views. For DESeq2 different stats
Great Question 2.1 years ago, created a question with more than 5,000 views. For Report and compare log2FC vs FC
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq vs DESeq2 have different DEGs results
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Report and compare log2FC vs FC
Popular Question 2.9 years ago, created a question with more than 1,000 views. For DESeq vs DESeq2 have different DEGs results
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Autobiographer 4.4 years ago, has more than 80 characters in the information field of the user's profile.

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