User: Bioinformatics_NewComer
Bioinformatics_NewComer • 320
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Posts by Bioinformatics_NewComer
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Answer:
A: Beagle imputation run time
... Are you doing this per chromosome?
Also, are you doing the imputation chromosome-wide? I think it is really hard computationally do run a chromosome wide imputation, rather it is suggested to perform imputation in chunks (3-5-7Mb however works). ...
written 5 months ago by
Bioinformatics_NewComer • 320
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... I've code and analysis pipeline developed on my end employing edgeR, limma, voom and other utilities. I'm reading and exploring when to use what and why, thus I thought to nudge this post because I'm confused and cannot understand further. Anyway, thanks~
...
written 9 months ago by
Bioinformatics_NewComer • 320
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... The end goal is simple differential gene expression analysis using case-control (human tissue). ...
written 9 months ago by
Bioinformatics_NewComer • 320
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... https://bioinformatics.stackexchange.com/questions/9172/how-are-residuals-used-as-new-phenotype
This may be of help to you.
...
written 9 months ago by
Bioinformatics_NewComer • 320
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... It is a great informative post. Thanks. I think I'm a bit confused with normalization here though.
When someone says or shares normalized data, do they share `cpm()` value or,
They scale their gene counts by `norm.factors` to generate normalized gene counts?
...
written 9 months ago by
Bioinformatics_NewComer • 320
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Comment:
C: RMA signal values
... Sorry to wake this arcane thread. What does the VALUE column tell? I'm looking around in vain with no documentation or manual, dictionary to assist.
...
written 12 months ago by
Bioinformatics_NewComer • 320
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... Hi - sorry to bump this ancient thread. I've been scratching my head over this for some time now.
What does 01/00 mean? If an individual in 1000G (Phase 3), for SNP1 has 00 haplotype what does it tell?
Thanks. ...
written 13 months ago by
Bioinformatics_NewComer • 320
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... ## ... Now use lm1$residuals instead of dat$y
Would you please be able to explain Why this residuals are used as new phenotype and how?
...
written 18 months ago by
Bioinformatics_NewComer • 320
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... Hi all,
I'm interested to use genegeneinteraction R package. For that data are read and a snp matrix is generated. When I try to run gene gene interaction I get error
GGI.res <- GGI(Y=Y, snpX=data$snpX, genes.info=data$genes.info,method="PCA")
Error:
> Error in GGI(Y = Y, snpX = data ...
written 23 months ago by
Bioinformatics_NewComer • 320
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Comment:
C: Help with SnpMatrix in R
... The link is dead. Am too looking for help with snpmatrix. ...
written 23 months ago by
Bioinformatics_NewComer • 320
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