User: Catalina Aguilar Hurtado

Reputation:
50
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Trusted
Location:
United States
Last seen:
8 months, 1 week ago
Joined:
4 years, 6 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 8 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 8 months ago by Catalina Aguilar Hurtado50 • updated 8 months ago by Aaron Lun21k
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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 8 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 8 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 8 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 8 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 8 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 8 months ago by Catalina Aguilar Hurtado50 • updated 8 months ago by Michael Love20k
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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 9 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 9 months ago by Catalina Aguilar Hurtado50

Latest awards to Catalina Aguilar Hurtado

Great Question 21 months ago, created a question with more than 5,000 views. For Report and compare log2FC vs FC
Popular Question 21 months ago, created a question with more than 1,000 views. For DESeq vs DESeq2 have different DEGs results
Popular Question 21 months ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Report and compare log2FC vs FC
Popular Question 2.6 years ago, created a question with more than 1,000 views. For DESeq vs DESeq2 have different DEGs results
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Autobiographer 4.1 years ago, has more than 80 characters in the information field of the user's profile.

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