User: Mozart
Mozart • 140
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Posts by Mozart
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Comment:
C: Is trimming always better?
... I see, thanks for clarifying this point. ...
written 21 days ago by
Mozart • 140
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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 ...
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... 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
Mozart • 140
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... Thanks so much, Jean-Karim. Very helpful.
regards, ...
written 5 weeks ago by
Mozart • 140
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... 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
Mozart • 140
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... 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$batch is required once you have your counts transformed (e.g. vsd) for visualisation purposes. So, ...
written 6 weeks ago by
Mozart • 140
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... Thanks so much for your reply; soon thereafter my thread I tried to add by myself this other column to my table and your reply comes as a confirmation for me. Thanks ...
written 6 weeks ago by
Mozart • 140
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... It really seems that you need to create the same identical column in sample table, too.
Thus, by doing this you should mange to solve the problem:
sampletable$batch=factor(c('1','1','2','2','3','3'))
if someone could confirm this, that would be great. thanks. ...
written 6 weeks ago by
Mozart • 140
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... 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+ ...
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... 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
Mozart • 140
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