User: Mozart
Mozart • 10
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- 10
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- 1 week, 4 days ago
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- 5 months, 4 weeks ago
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Posts by Mozart
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Comment:
C: Paired t-test with DESeq2
... Thanks for your reply.
I am wondering how one could perform t-test with DESeq2. Don't know the code, unfortunately. ...
written 11 days ago by
Mozart • 10
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Comment:
C: Paired t-test with DESeq2
... Thanks ATpoint; I realised I made a mistake in the writing of this post. I meant to say that there's indeed a correlation between genes found with this approach (t-test) and qpcr. That's the rationale behind this post.
thanks. ...
written 12 days ago by
Mozart • 10
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... Hello there,
I know you are not recommending to perform t-test when doing rna-seq but I really need to know how to perform the latter because the core facility who analysed my samples did this and apparently don't want to disclose the code used at this stage. The reason why I am so keen is that, whe ...
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... hello there,
I am not fully sure what I am doing here.
Basically, I have always known that when using tsv files, there should not be any inferential replicates considered. But now, in the latest version of tximport, I guess something has changed?
> txi.kallisto.tsv <- tximport(files, type ...
written 4 months ago by
Mozart • 10
• updated
4 months ago by
Michael Love ♦ 25k
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... Sorry, I only see this mirroring effect only after using Limma::removeBatchEffect function. ...
written 4 months ago by
Mozart • 10
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... Thanks for your reply Michael.
from your last question:
dim (dds)
returns ~30000 rows and 12 columns
by not including batch variable in the design (i.e. just ~condition in the dds object) and doing the following
vsd <- vst(dds)
x = assay(vsd)
I have some funny results, for ex ...
written 4 months ago by
Mozart • 10
0
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... **oh, sorry Michael,** I have just noticed that I got my **first question** truncated for some reasons. Would you mind to re-read the above post, please? thanks ...
written 4 months ago by
Mozart • 10
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... Hi Michael,
sorry for re-upping this post but I may want to ask you further clarification about how to deal with this batch effect in DESeq2. My understanding tells me that when we want to control the batch effect in differential expression analysis with just need to include batch factor in the desi ...
written 4 months ago by
Mozart • 10
0
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Comment:
C: Principal components in DESeq2
... Thanks Kevin,
now I have understood why this DESeq2 plot is defined 'biased'. So, rather than doing the code above I could simply do in the following way:
rv <- rowVars(assay(rld))
p <- pca(x, metadata = NULL, removeVar = NULL)
p$rotated[,1:2]
Is this what you were referring to? ...
written 4 months ago by
Mozart • 10
2
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... Dear Michael,
when it comes to analyse different comparisons in a complex experimental design, generally speaking, there are two apparent solutions:
1. first one is to consider the whole experiment (i.e. using just one Sample table containing all the samples) and write a string of code to select de ...
written 4 months ago by
Mozart • 10
• updated
4 months ago by
Michael Love ♦ 25k
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