User: Lila M
Lila M • 860
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Posts by Lila M
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... Dear all,
I'm working with metagenomic data (OTUs). I've alreade have the zero inflated matrix and an aditional matrix with more than 80 covariates. By using MaAsLin (https://github.com/biobakery/Maaslin2) I would like to identify the significant metagenomic species associated with clinical covarie ...
written 13 months ago by
Lila M • 860
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... Is the third time that I got this answer. I explained why I want to do that. Please, add I comment if you could give any new feedback ...
written 14 months ago by
Lila M • 860
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... Sorry, the "add comment" button doesn't work for me, it gives me an error all time, so this is why I used the "add comment".
Lets say I have a data frame like this
ID group gene1 gene2 gene3...
s1 health 0.1 0.07 0.2
s2 cancer0.5 0.05 0.4
and I have 20 healthy samples and 40 cancer sa ...
written 14 months ago by
Lila M • 860
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... Hi, I know how to do that in limma. The point is, that I want to create a function to apply it to a gene table, OTU table... in other words to extrapolate to different approach. Any clue?
Thanks! ...
written 14 months ago by
Lila M • 860
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... Dear all,
I have a data set for two condition (before and after treatment). The patients are in rows and the gen expression in levels. I want to compare if there is any different in treatment, but the main problem that I have is the unbalanced samples (control 30:case 60).
I would like to re-sampl ...
written 14 months ago by
Lila M • 860
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... I'm trying to find the best way to represent some microbiome data. First of all I've created a model using [ZIBR][1] so I can catch the abundance differences in my species regarding different condition.
The "problem" that I have now is that I am trying to do a boxplot for different condition and as ...
written 15 months ago by
Lila M • 860
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Comment:
C: How to analyze aCGH data in R?
... Hi Kevin, and thank you for your feed back. Yes I've checked it and found something related with `Agilent4x44K Arrays` however, this experiment is `CGH array (4X180K)` so I could not find something related with CGH arrays, any clue about how to start with it?
Thanks! ...
written 15 months ago by
Lila M • 860
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... Dear all,
I've tried to analyze this [data][1] that is a aCGH data in R. But I couldn't find any tutorial that can help me to import data and everything.
Any idea?
Thank you
[1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36864 ...
written 15 months ago by
Lila M • 860
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... Hi all,
I'm trying to summarize some longitudinal data that looks like this:
ID Time_point treatment
20 4 Treated
20 7 Treated
20 9 Treated
20 12 Treated
20 21 Treated
28 4 No Treated
28 7 No Treated
...
written 16 months ago by
Lila M • 860
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... Hi all,
I'm trying to apply `Dirichlet-multinomial mixture model` over some `Bracken`(ayesian Reestimation of Abundance with KrakEN) specie abundance in two different condition: treated and not treated in two different data frames (rows as patient ID and cols as ssp).
What I did first is to remove ...
written 16 months ago by
Lila M • 860
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