User: Mozart

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Mozart140
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Posts by Mozart

<prev • 79 results • page 1 of 8 • next >
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Comment: C: Is trimming always better?
... I see, thanks for clarifying this point. ...
written 21 days ago by Mozart140
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Forum: Is trimming always better?
... Hello there, it may sound naive but sometimes people I know tend to avoid trimming step (i.e. using Trimmomatic) when 1. the software which convert raw BCL data manages to remove adapters and 2. alignment rate is more than 50% what you think? thanks ...
trimmomatic trimming qc forum rna-seq written 21 days ago by Mozart140 • updated 21 days ago by genomax69k
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Comment: C: Using bootstrap testing in kallisto to obtain estimated transcript counts
... Sorry for re-upping this post. Can I ask you if in the newer version of Kallisto, inferential replicates are taken into account also when using .tsv files? Because when I am importing tsv files with tximport, it says: Note: importing `abundance.h5` is typically faster than `abundance.tsv` ...
written 29 days ago by Mozart140
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Comment: C: Is hierarchical clustering of significant genes 'supervised' or 'unsupervised' c
... Thanks so much, Jean-Karim. Very helpful. regards, ...
written 5 weeks ago by Mozart140
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Comment: A: Is hierarchical clustering of significant genes 'supervised' or 'unsupervised' c
... Sorry for re-upping this post (it is always better than creating a new thread, I guess). So, if I got it right: 1. when you extract RNA from samples (let's say treated with something or even a specific phenotype) **and**, 2. when you have your genes annotated, **and** you're asking how these gene ...
written 5 weeks ago by Mozart140
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Comment: C: adding batch variable in colData(dds)
... Hi and thanks for your reply. Literally I got confounded by the double approach to deal with batch effect in DESeq2 because, reading the manual and other posts on bioconductor and here, apparently dds$batch is required once you have your counts transformed (e.g. vsd) for visualisation purposes. So, ...
written 6 weeks ago by Mozart140
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Comment: C: adding batch variable in colData(dds)
... Thanks so much for your reply; soon thereafter my thread I tried to add by myself this other column to my table and your reply comes as a confirmation for me. Thanks ...
written 6 weeks ago by Mozart140
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Comment: C: adding batch variable in colData(dds)
... It really seems that you need to create the same identical column in sample table, too. Thus, by doing this you should mange to solve the problem: sampletable$batch=factor(c('1','1','2','2','3','3')) if someone could confirm this, that would be great. thanks. ...
written 6 weeks ago by Mozart140
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adding batch variable in colData(dds)
... Dear all, I am quite struggling with some sort of coding here. Essentially, what I am trying to do is to simply add the batch variable to my design in DESeq2. Thus, I am doing: dds$batch = factor(c('1','1','2','2','3','3')) dds <- DESeqDataSetFromTximport(txi.kallisto.tsv, table, ~batch+ ...
deseq2 written 6 weeks ago by Mozart140 • updated 6 weeks ago by prabin.dm160
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Answer: A: Batch effect, how to create a model matrix
... Thanks both of you, guys. These suggestions really help myself to clarify this complex problem that I know it is kind of uncertain also amongst the advanced users. Thanks. This is directly linked to both of your replies as I am really trying to understand how I can efficiently design a formula by i ...
written 7 weeks ago by Mozart140

Latest awards to Mozart

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Kallisto-Sleuth or Kallisto-Deseq2?
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For PCA in a RNA seq analysis
Appreciated 7 months ago, created a post with more than 5 votes. For PCA in a RNA seq analysis
Great Question 8 months ago, created a question with more than 5,000 views. For PCA in a RNA seq analysis
Prophet 8 months ago, created a post with more than 20 followers. For PCA in a RNA seq analysis
Popular Question 9 months ago, created a question with more than 1,000 views. For Kallisto or Deseq2?
Student 9 months ago, asked a question with at least 3 up-votes. For PCA in a RNA seq analysis
Popular Question 12 months ago, created a question with more than 1,000 views. For Kallisto or Deseq2?
Popular Question 16 months ago, created a question with more than 1,000 views. For PCA in a RNA seq analysis
Supporter 20 months ago, voted at least 25 times.

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