## User: PJ

PJ •

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#### Posts by PJ

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Comment:
C: metagenomeSeq log transformation

... Yes, you are right. I added a second normalization step based on reference gene length and 16S bacterial reads so I am not using the read counts. Could this affect the statistical output? Where can I see the actual formula to calculate average expression? Thanks again!
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written 2.8 years ago by
PJ •

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Comment:
C: metagenomeSeq log transformation

... Thanks Joseph for the quick answer. What about the negative tansformed log values? Is the program taking the absolute values for statistics?
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written 2.8 years ago by
PJ •

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Comment:
C: metagenomeSeq log transformation

... In addition, how is it possible that features with negative log2 values in the transformed count matrix come up with positive average expression values in the statistical output? Thanks!
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written 2.8 years ago by
PJ •

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... Hi,
Normalized counts from the matrix table are transformed to log2 values by metagenomeseq, aren´t they? My question is about the zeros in the count matrix. How are they transformed to allow statistical analysis? (as log2 of zero gives an error). Thanks!
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written 2.8 years ago by
PJ •

**0**• updated 2.8 years ago by Joseph Nathaniel Paulson •**280**1

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... Hi everybody,
I have a model with 2 main factors and its interaction:
designmodel = model.matrix(~0 + Factor1 + Factor2 + Factor1:Factor2)
Factor 1 has two levels and factor 2 has 4 levels. My question is if when I test the interaction term I can add all 8 groups as follow:
contrastInteraction ...

written 3.4 years ago by
PJ •

**0**• updated 3.4 years ago by Gordon Smyth ♦**39k**0

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... Does metagenomeSeq handle mixed models including random effects? If yes, how can I incorporate those random effects in the model?Thanks!
...

written 3.8 years ago by
PJ •

**0**• updated 3.8 years ago by noelle.noyes •**30**0

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... Hi,
My experimental model is repeated measures with 2 fixed effects and 1 random effect. How can I specify that in the model statement? I am having a hard time trying to figure it out.
Thanks!
...

written 4.1 years ago by
PJ •

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... Hi,
I am creating a heat map based on the following script:
trials=pData(object)$treatment
heatmapColColors=brewer.pal(12, "Set3")[as.integer(factor(trials))] heatmapCols=colorRampPalette(brewer.pal(9, "RdBu"))(50)
plotMRheatmap(obj=object, n=6, cexRow=0.4, cexCol=0.4, trace="none", col=heatmap ...

written 4.5 years ago by
PJ •

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... Hi,
I am running fitZig for differential abundance testing. When I place:
treatment=pData(obj)$Treatment
Before=pData(obj)$Time
normFactor=normFactors(obj)
normFactor=log2(normFactor/median(normFactor)+1)
mod = model.matrix (Treatment + Before + normFactor), the answer is:
Error: $ operator i ...

written 4.5 years ago by
PJ •

**0**• updated 4.5 years ago by Hector Corrada Bravo •**60**#### Latest awards to PJ

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