User: Mozart

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Mozart240
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Posts by Mozart

<prev • 132 results • page 1 of 14 • next >
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Network analysis: where to start?
... Hello there, I am really fascinated by the possibility to start developing a very simple tool for analysing networks, given a list of genes. firstly, I would like to stress that the aim is not to publish but just understand the basics needed to get into grip with this tool. Before posting, I have r ...
network analysis rna-seq written 1 day ago by Mozart240 • updated 1 day ago by Bogdan1.0k
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Comment: C: PCA plots and biological information taken from other principal components
... Sorry for resurrecting this old post. I am always referring to this dataset where it seems that a nice clustering between groups is mainly achieved when PC5 is plotted against PC6. This is really a curiosity-driven question but would it be possible somehow to *extract and determine* which genes are ...
written 16 days ago by Mozart240
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Convergence of betas, iterations arguments with nbinomialWaldTest
... Hi, I am not going to ask how to solve issue related to the maxit argument with nbinomialWladTest within DESeq2 but for me, far from this scientific field, it's really hard to go through the vignette, other posts and lessons and trying to end up with a clear explanation of what is the convergence of ...
rna-seq written 19 days ago by Mozart240
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Comment: C: List of uniquely expressed genes
... Thank Kevin for your reply. Very helpful. My big concern here would be not only to define a parameter that define unique expression but also how to discriminate between different groups, if you get me. For example, what if a sub-group gets a z-score of 10, other two 5, and one 2? How can you set a c ...
written 9 weeks ago by Mozart240
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Comment: C: List of uniquely expressed genes
... Thanks a lot Kevin for this. Can I ask you if could explain why z score have to be bigger than 1.96 and what's its relationship with the mean value, please? To be fair I don't have an idea the rationale behind using z-scores? I presume we can use it because it returns standardised measurements? than ...
written 10 weeks ago by Mozart240
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Comment: C: List of uniquely expressed genes
... Thanks for your comment. They are trying to determine uniquely expressed genes that are taken from of a certain dataset. They want me to create a set per group containing gene that characterise the latter. Do you have any idea how to deal with this? Apparently, as far as I am aware a relative compar ...
written 10 weeks ago by Mozart240
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List of uniquely expressed genes
... Dear all, I am wrapping my head around a way to define uniquely expressed genes regardless of any differential expression analysis approaches. Essentially, it has been asked to find some sort of 'method' that allowed me to define a certain gene as uniquely expressed in the dataset in such way that I ...
counts rna-seq written 10 weeks ago by Mozart240
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Meta Analysis on RNA-seq data
... Hello there, 1. I was reading this [post][1] and wondering what could be the best tool to perform meta-analysis for RNA-seq experiment. Is DESeq2 a good tool for that? I have heard about metaSeq and it seems to be good. Any experience with the latter, by any chance? 2. anothe ...
meta analysis rna-seq written 12 weeks ago by Mozart240 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: "Enhanced Volcano" package - how to set p adjusted cut off?
... thanks a lot for that! ...
written 3 months ago by Mozart240
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Comment: C: "Enhanced Volcano" package - how to set p adjusted cut off?
... Kevin, sorry for resurrecting this old post. Not sure I have got this right. In the default settings, the parameter `pCutoff` stands for nominal p value, right? what if one wants to use p adjusted ones, instead? Sorry for my naive question but, why in a volcano plot nominal p values are preferred o ...
written 3 months ago by Mozart240

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For biomaRt correct annotation but...
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