User: piensaglobalmente

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Australia
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Posts by piensaglobalmente

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Seeking confirmation on manually setting contrasts for a 3-factor design in DESe
... Thank you Michael. I can keep looking through the glmm literature now that you confirm that contrasts in DESeq2 and other negative binomial models are specified the same. I just wasn't sure if there was some unique DESeq2 functionality I wasn't finding that would draw out these contrasts.   cheers, ...
written 17 months ago by piensaglobalmente10
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Seeking confirmation on manually setting contrasts for a 3-factor design in DESeq2 with multiple interaction terms
... Hello, I am seeking confirmation on manually setting contrasts for a 3-factor design in DESeq2 with multiple interaction terms I have a 3-factor experiment, with each factor containing 2 levels: Type: Juvenile vs Sediment Shore: Inshore vs Offshore Sector: North vs Central I am interested in t ...
deseq2 design and contrast matrix interactions contrast multiple factor design written 17 months ago by piensaglobalmente10 • updated 17 months ago by Michael Love13k
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Comment: C: Interpretation of intercept-only model (~1) in DESeq2
... Thank you so much for the quick, clear and thorough answers!!  ...
written 18 months ago by piensaglobalmente10
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Interpretation of intercept-only model (~1) in DESeq2
... Hi, I am looking for a bit more information on what exactly the intercept-only model represents in DESeq2, ie, when you set the experimental design formula to ~1 (without predictors)? Potential interpretations: 1) Would you expect that the baseMean output values would represent the simple average ...
phyloseq deseq2 written 18 months ago by piensaglobalmente10 • updated 18 months ago by Michael Love13k
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Comment: C: Inputting counts of zero into DESeq2
... Thank you Michael! ...
written 2.2 years ago by piensaglobalmente10
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Answer: A: Inputting counts of zero into DESeq2
... Hi Michael, Thank you for your responses! Therefore, the following two methods should be equivalent to estimate VST counts (well the DESeq call allows you to go on and do differential expression testing). # calculate geometric means prior to estimate size factors gm_mean = function(x, na.rm=TRU ...
written 2.2 years ago by piensaglobalmente10
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Comment: C: Inputting counts of zero into DESeq2
... Hi Michael, Sorry for the late reply!! I had to confirm by email address.... I am principally using DESeq through the Phyloseq() package (http://joey711.github.io/phyloseq-extensions/DESeq2.html). I am using DESeq for two reasons: 1) I would like to use DESeq to perform VST. I can then use the ta ...
written 2.2 years ago by piensaglobalmente10
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Answer: A: Inputting counts of zero into DESeq2
... I noticed an odd result after running the following Deseq2 commands through phyloseq: ``` packageVersion("phyloseq") #[1] ‘1.10.0’ test2<-otu_table(test, taxa_are_rows=TRUE) testvar2<-sample_data(testvar) testtot<-merge_phyloseq(test2, testvar2) deseq2<-phyloseq_to_deseq2(testtot, ~1) ...
written 2.3 years ago by piensaglobalmente10

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