User: tiphaine

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tiphaine10
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European Union
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4 years ago
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Posts by tiphaine

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Comment: C: RNA-seq Data Normalisation methods on samples associated with a global modificat
... thanks, I run to read it ! ...
written 4.1 years ago by tiphaine10
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Comment: A: RNA-seq Data Normalisation methods on samples associated with a global modificat
... Thank Devon,  1. Unfortunately (fortunately depending on the point of view), I have a mostly unidirectional global shift and it is on tissue and not on single cell-type. I am going to look at ERCC spike-ins and if it is possible to apply for other omic data. I hope it is not so hard to use deal wit ...
written 4.1 years ago by tiphaine10
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RNA-seq Data Normalisation methods on samples associated with a global modification
... Dear all, I would like to use the same method to normalise and analyis the differential expression for not only RNA-seq data but also for other sequencing count data such as 16S and epigenetics data. But if I look at the high level of my omic data, it seems that there is a global modification betw ...
count data global modification deseq2 limma edger written 4.1 years ago by tiphaine10
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Comment: C: DESeq2: can I correct for relatedness when using data from multiplex families?
... Ok, thanks. I am going to reads the papers to be sure about my models because I thought to use it the same protocol for my different omic data that are generated into tables of per-feature counts for each sample such as microbiome . ...
written 4.1 years ago by tiphaine10
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Comment: C: DESeq2: can I correct for relatedness when using data from multiplex families?
... Oh, I didn't know that. I am going to look at that and maybe I come back to you if I am not sure to do. do you have a link that explains that. thanks ...
written 4.1 years ago by tiphaine10
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Comment: C: DESeq2: can I correct for relatedness when using data from multiplex families?
... thanks for this currently, I uses lmer4 with a random effect for zygosity and family. So I can use DESeq to normalise my data but not to find the differential expression.   ...
written 4.1 years ago by tiphaine10
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Comment: C: DESeq2: can I correct for relatedness when using data from multiplex families?
... Currently, I have two cases. One model where I have only twin pairs (DZ and MZ) and another model where I have a mixture of twin pairs and singles but I know whether they are MZ or DZ. I have not yet other individuals in my family. It is more for my curiosity to know how to deal it too.       ...
written 4.1 years ago by tiphaine10
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DESeq2: can I correct for relatedness when using data from multiplex families?
... Hi All. My question is the same blood than this post https://www.biostars.org/p/129109/#130906  In your solution, the model takes care only if the samples belong to the same family. I would like to know how we can add the level of relatedness such as MZ twin (100%) and DZ twin (50%). Currently, I ...
relatedness deseq2 rna-seq written 4.1 years ago by tiphaine10 • updated 4.1 years ago by Devon Ryan88k
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Comment: C: DESeq2: can I correct for relatedness when using data from multiplex families?
... Hi, In your solution, the model takes care only if the samples belong to the same family. I would like to know how we can add the level of relatedness such as MZ twin and DZ twin. Currently, I have a variable zygosity with 2 levels (MZ and DZ). Do you thus suggest to use the following model? ​~ ...
written 4.1 years ago by tiphaine10

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