User: iraia.munoa
iraia.munoa • 60
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Posts by iraia.munoa
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... Ok, thanks Kevin. It was more a thing of understanding correctly the way David works, as I did not find anything about it in their manual. Thanks!! ...
written 2 days ago by
iraia.munoa • 60
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... Hi everybody,
I am using david ontology functional annotation clustering. The thing is that it results very few biological function groups and in the bottom of the page there is a a square saying " 54 terms were not clustered".
What does it mean? I guess that the functional annotation clustering onl ...
written 21 days ago by
iraia.munoa • 60
• updated
20 days ago by
Kevin Blighe ♦ 37k
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... Hi everybody!
I was wondering if there is a need of normalizing read coverage when converting bam results to bedgraph or bigwing for RNA-seq sample visualization.
I have used TMM normalization for RNA-seq DEGs analysis and I want to visualize this results in UCSC genome browser.
I have been reading ...
written 5 weeks ago by
iraia.munoa • 60
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... And is it possible to add variance % explained por PC1 and PC2 in the axes? ...
written 6 weeks ago by
iraia.munoa • 60
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... Thanks Gordon! I didn't know it was as easy as that! I also will have into account the term prior.count when doing logcpm values. I have seen your explanation in support.bioconductot, so everything is clear now. I am really happy that you guys concers about helping beginers with your knowledge, Than ...
written 6 weeks ago by
iraia.munoa • 60
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... I didn't know about "prior.count". I have read what Gordon says in the post you linked, and I have used it in my samples, and the MDSplot looks the same.
I don't understand really well why I should use it. It is to avoid that 0 counts become Inf when doing the log transformation? And how do I know ...
written 6 weeks ago by
iraia.munoa • 60
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... Thanks again for all your answers, you have helped me a lot!
If someone more wants to add some other points of view they are also welcome to writ in this post.
What about the variance values? Are they enough to focud on PC1 vs PC2 or do I need to change to PC3 or something like that? ...
written 6 weeks ago by
iraia.munoa • 60
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... To follow with RamRS answer, I didn't know the need to transpose the count matrix, and I simply followed a pipeline posted in my first reply. I though that it was correct to use it as a global value for each variables, as they explain the rotations value as coefficients of the linear combinations o ...
written 6 weeks ago by
iraia.munoa • 60
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... Oh! sorry, with my coments I did not want you to say if everything I have done is correct or not. I only want recomendation of which steps to follow or detection if something I have shown here is correct or not. I mean, we don't have bioinformaticians in our research group, so I am trying to underst ...
written 6 weeks ago by
iraia.munoa • 60
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... Hi again!
I think I have manage to follow your recomendations. I write them right here to see if I am correct (after TMM normalization, log transformation and removing batch effect):
> TMM_ApCTRvsPIR <- calcNormFactors(d_ApCTRvsPIR_filt, method="TMM")
> batch <- factor(substring ...
written 6 weeks ago by
iraia.munoa • 60
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For How to see if adjusting batch effect in RNA-seq is working or not
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