User: SPbeginner

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Posts by SPbeginner

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Comment: C: limma voom - time course experiment - multi level experiment
... Thank you so much for your explanation. Now it's much more clear. In my case, using duplicateCorrelation() blocking on each animal calculate the correlation measurements made on the same animal, this is why we do not expect a high value (due to experimental condition) is it ? ...
written 6 months ago by SPbeginner0
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limma voom - time course experiment - multi level experiment
... Dear Bioconductor community, I'm analyzing RNA-seq data with limma-voom. This experiment involves 6 subjects, including 3 animals who dead after infection by a virus and 3 animal who survive. From each subject, blood were collacted before any treatment (D0) and at different time points after infe ...
limma duplicatecorrelation limma voom written 6 months ago by SPbeginner0 • updated 6 months ago by Gordon Smyth35k
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Comment: C: limma - Multi-level Experiments - time course data
... Animals are supposed to be the same (same sex + same age, all coming from the same farm).  ...
written 8 months ago by SPbeginner0
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Comment: C: limma - Multi-level Experiments - time course data
... The Group A and D received an attenuated form of a virus whereas Group F received the virus. So A and D are close whereas F is really different.  So i'll include animal in the model matrix as Aaron Lun suggest : design <- model.matrix(~0 + Animal + Group, Design_clean_simple) design <- desi ...
written 8 months ago by SPbeginner0
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limma - Multi-level Experiments - time course data
... Dear Bioconductor community, I have a two-way experiment in which time course profiles are to be compared for two many groups. Consider the target frame : Group Animal A.0 A657 A.0 A777 A.0 B369 A.0 B382 A.0 B401 A.0 B433 A.3 B401 A.3 A657 A.3 A777 A.3 B369 A.3 B382 A.3 B433 A.7 A657 A.7 A777 A. ...
limma deg rnaseq_analysis limma voom written 8 months ago by SPbeginner0 • updated 8 months ago by Aaron Lun21k
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Comment: C: Limma : time course experiment with missing data
... Is it a problem to use Limma with blocked model when the dataset contain 2 groups with time points that are different ? As an example, I have Group A with D0,D3,D7 and D27 and Group B with D0,D1,D3,D5,D7 and D28 ? I would like to identify genes which respond differently over time in the different g ...
written 8 months ago by SPbeginner0
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Comment: C: Limma : time course experiment with missing data
... So, for you, my code is correct ? I'll try to use splines for between-group comparison and let you know ! ...
written 8 months ago by SPbeginner0
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Comment: C: DESeq2 : group specific effect of a treatment while controlling for individual e
... How can I analyse these data with DESeq2 ?  Am I correct : TS <- paste(Design_clean$Treatment, Design_clean$Time, sep=".") Design_clean_simple <-data.frame(Group=TS,Animal=factor(Design_clean$Animal),row.names=row.names(Design_clean)) dds <- DESeqDataSetFromMatrix(countData = Count, colD ...
written 8 months ago by SPbeginner0
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Comment: A: DESeq2 : group specific effect of a treatment while controlling for individual e
... I have another question. I have the same kind of RNA-seq data to analyse, but this time, each subject doesn't yields a value at each time point. I have animal with missing data at some time points Can I still set this design ?  design=~Treatment+Treatment:ind.n+Treatment:Time ...
written 8 months ago by SPbeginner0
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Limma : time course experiment with missing data
... Dear Bioconductor community, I have timecourse RNA-seq data. Some sample are low quality (high RNA degradation, low coverage on genes), this is why I wanted to use limma-voom with  voomWithQualityWeights Animals received 2 differents treatments (TreatmentA, TreatmentB). There are different num ...
limma limma-voom written 8 months ago by SPbeginner0

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