User: Catalina Aguilar Hurtado

Reputation:
50
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Trusted
Location:
United States
Last seen:
2 weeks, 5 days ago
Joined:
5 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 • 44 results • page 1 of 5 • next >
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library normalization for DESeq2 using mapping proportions
... Hi I have a RNAseq dataset that is a mix of related symbiont algae species, that change in proportions with the treatment. I would appreciate any advice on a method that I can use to normalize these rnaseq libraries based on the fraction of reads per sample. I already know the proportion of each sp ...
normalization deseq2 written 24 days ago by Catalina Aguilar Hurtado50 • updated 22 days ago by Michael Love26k
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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 21 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 21 months ago by Catalina Aguilar Hurtado50 • updated 21 months ago by Aaron Lun25k
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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 21 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 21 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 21 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 21 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 21 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 21 months ago by Catalina Aguilar Hurtado50 • updated 21 months ago by Michael Love26k
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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 22 months ago by Catalina Aguilar Hurtado50

Latest awards to Catalina Aguilar Hurtado

Great Question 12 months ago, created a question with more than 5,000 views. For Report and compare log2FC vs FC
Epic Question 12 months ago, created a question with more than 10,000 views. For Report and compare log2FC vs FC
Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2 different stats
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Popular Question 2.8 years ago, created a question with more than 1,000 views. For DESeq vs DESeq2 have different DEGs results
Great Question 2.8 years ago, created a question with more than 5,000 views. For Report and compare log2FC vs FC
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeq vs DESeq2 have different DEGs results
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Report and compare log2FC vs FC
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Heatmap from DESeq2 DE genes
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.

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