User: rmf

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rmf110
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Posts by rmf

<prev • 87 results • page 1 of 9 • next >
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Comment: C: RNA-Seq DGE: Evaluate model quality
... @Devon Yep `~family + condition` is my current choice. Sure, I could just do that and move on. But, I am just curious how the other models work. All I have at the moment to evaluate this is the number of DEGs found. I am trying to find out if there is a better metric that I could use to evaluate whi ...
written 5 hours ago by rmf110
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Comment: C: RNA-Seq DGE: Evaluate model quality
... @Kevin The general suggestion is that I use `family+condition`. I do get your explanation behind it. But, I would still like to know how one would evaluate these models. How do I know which model gives me the 'correct' set of DEGs. Is there some metric that I could use to decide model is better? For ...
written 6 hours ago by rmf110
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RNA-Seq DGE: Evaluate model quality
... I am using DESeq2 to find differentially expressed genes between conditions control/treated. The PCA using vst counts shows family-based clustering. ![enter image description here][1] I have conjured up a few different GLM models as below along with the number of differentially expressed genes det ...
deseq2 rna-seq differential gene expression written 11 hours ago by rmf110 • updated 6 hours ago by Devon Ryan76k
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Comment: C: RNA-Seq DGE using PCA components as covariate
... The formula is used in DESeq2. Perhaps I should've mentioned that somewhere. ...
written 1 day ago by rmf110
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Comment: C: RNA-Seq DGE using PCA components as covariate
... Thanks for the insight. This is exactly the sort of input I was looking for. And yes, the plot was done in R (ggplot) :-) ...
written 1 day ago by rmf110
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Comment: C: RNA-Seq DGE using PCA components as covariate
... @Kevin Thanks for the input. Yes, I did get the idea from GWAS. I am a bit confused by some part of your comment. '...there is no confounding.' In this dataset, I am looking for DEGs between case and control. I am not interested in families. So I would say family is a confounding effect. The famil ...
written 1 day ago by rmf110
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Comment: C: RNA-Seq DGE using PCA components as covariate
... Yes, they do cluster fairly well by family, hence the need for family correction. By 'heterogeneity', I mean to say that the individuals are quite spread out within families and not exactly forming a small tight cluster. This is the reason why I was wondering if a PCA covariate approach might be bet ...
written 1 day ago by rmf110
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RNA-Seq DGE using PCA components as covariate
... I am interested in finding differentially expressed genes between conditions control/treated. But, I need to control for family-level variation in my GLM model. My initial approach was `~family+condition`. Based on my PCA, I think my family structure is too heterogenous. ![enter image description ...
deseq2 rna-seq differential gene expression glm written 1 day ago by rmf110 • updated 1 day ago by h.mon11k
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Comment: C: deflated lambda value but inflated qq plot
... I have the reverse situation. Strange indeed! ...
written 13 days ago by rmf110
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Comment: C: How Does Ld In Plink Work?
... So `--ld-window-kb` specifies the window in which to compare snps. What is `--ld-window 99999`? ...
written 15 days ago by rmf110

Latest awards to rmf

Scholar 22 days ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Voter 11 weeks ago, voted more than 100 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 6 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 15 months ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
Student 15 months ago, asked a question with at least 3 up-votes. For Consequences of degraded DNA for Sequencing
Scholar 15 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Supporter 21 months ago, voted at least 25 times.

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