User: narges

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narges180
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Finland
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Posts by narges

<prev • 71 results • page 1 of 8 • next >
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Comment: C: Limma For Rna-Seq Analysis
... Actually I found this unpublished one. I did not go through it but from the title I expected it is regarding the "voom" which I think is a method of normalization but not testing for differential expression. Is it correct or it tests the DE as well? ...
written 6.2 years ago by narges180
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Limma For Rna-Seq Analysis
... Hi, I want to use Limma for RNA-seq analysis. Its manual in Bioconductor includes a section for RNA-seq case of study but the main paper I can find regarding the limma is for year 2004 which is explaining limma only for microarray. Does any one knows if there is a more recently publication or any o ...
limma rna-seq written 6.2 years ago by narges180 • updated 6.2 years ago by Devon Ryan93k
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... Based on your example, can I assume the situation you mentioned is something different to "sequencing depth" bias. So, now I think we can have technical variabilities because of different sequencing depth between samples. Moreover, we can have technical veriablities because of sampling different num ...
written 6.3 years ago by narges180
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... I was wondering if I could ask one more question or it would be impolite. Just to be sure I wanted to ask does this mean that the sequencing machine may remove the "RNA composition" bias in some sense. However, many many thanks I learned a lot. ...
written 6.3 years ago by narges180
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... Thanks a lot. I wanted to ask if you could suggest me any further resource to read more about this concept or not. ...
written 6.3 years ago by narges180
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... Sampling bias. Do you mean technical biases which are available when extracting RNA molecules from the cell? ...
written 6.3 years ago by narges180
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... Actually based on the paper section you mentioned and the example, I some how understand we should not use only the raw library size as the normalization factor. But I do not understand why necessarily increase in one gene should lead to decrease in another. Otherwise I think now I understand what y ...
written 6.3 years ago by narges180
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... Are you sure that your sample is reformulating the example in the paper? Based on my understanding, in the paper example, it intends to say the total number of RNA reads in one group should be two times of the other group so we should have factor of 2. But in your example the total library size for ...
written 6.3 years ago by narges180
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... yes exactly I was mentioning that part. ...
written 6.3 years ago by narges180
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Comment: C: Rna Composition Bias In Rna-Seq Analysis
... No, I did not mean GC content. I think GC content does not affect the results very much as it could be some how the same for all libraries. But i meant the RNA composition bias that for example we use calcNormFactors() method in edgeR to eliminate it. I meant I expected that we use calcNormFactors() ...
written 6.3 years ago by narges180

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