User: Mozart
Mozart • 10
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Posts by Mozart
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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 5 weeks ago by
Mozart • 10
• updated
5 weeks ago by
Michael Love ♦ 24k
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... Sorry, I only see this mirroring effect only after using Limma::removeBatchEffect function. ...
written 6 weeks 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 6 weeks ago by
Mozart • 10
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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 6 weeks 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 7 weeks ago by
Mozart • 10
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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 7 weeks ago by
Mozart • 10
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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 7 weeks ago by
Mozart • 10
• updated
7 weeks ago by
Michael Love ♦ 24k
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Comment:
C: Principal components in DESeq2
... So, you can confirm that apart from the 'intgroup.df' everything is fine? ...
written 7 weeks ago by
Mozart • 10
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... Hello there,
after reading a few posts here about this particular topic, I guess I solved this 'puzzling' issue and I just need to check that this is the correct way to do this. Essentially, I need to output the PC1 and PC2 from plotPCA function in order to let someone else to play around with an ex ...
written 7 weeks ago by
Mozart • 10
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... Yes, I do agree with you Michael. Surely, the best thing to do is taking some courses for this, at the moment, I only have a smattering of stats not being my background. I hope this time my question will sound more DESeq2-related as I am still unsure whether or not putting batch in the design formul ...
written 8 weeks ago by
Mozart • 10
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