## User: PJ

PJ0
Reputation:
0
Status:
New User
Last seen:
2 years, 10 months ago
Joined:
4 years, 5 months ago
Email:
p******@colostate.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

#### Posts by PJ

<prev • 9 results • page 1 of 1 • next >
1
634
views
1
... 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! ...
written 2.8 years ago by PJ0
1
634
views
1
... Thanks Joseph for the quick answer. What about the negative tansformed log values? Is the program taking the absolute values for statistics?  ...
written 2.8 years ago by PJ0
1
634
views
1
... 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! ...
written 2.8 years ago by PJ0
1
634
views
1
... 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! ...
written 2.8 years ago by PJ0 • updated 2.8 years ago by Joseph Nathaniel Paulson280
1
735
views
1
... 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 PJ0 • updated 3.4 years ago by Gordon Smyth39k
2
796
views
2
... 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 PJ0 • updated 3.8 years ago by noelle.noyes30
0
514
views
0
... 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 PJ0
0
613
views
0
... Hi,  I am creating a heat map based on the following script: trials=pData(object)$treatment heatmapColColors=brewer.pal(12, "Set3")[as.integer(factor(trials))] heatmapCols=colorRampPalette(brewer.pal(9, "RdBu"))(50) plotMRheatmap(obj=object, n=6, cexRow=0.4, cexCol=0.4, trace="none", col=heatmap ... written 4.5 years ago by PJ0 1 answer 879 views 1 answer ... Hi, I am running fitZig for differential abundance testing. When I place: treatment=pData(obj)$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 PJ0 • updated 4.5 years ago by Hector Corrada Bravo60

#### Latest awards to PJ

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.