## User: SPbeginner

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#### Posts by SPbeginner

<prev • 18 results • page 1 of 2 • next >
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... 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 3 months ago by SPbeginner0
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... 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 ...
written 3 months ago by SPbeginner0 • updated 3 months ago by Gordon Smyth35k
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... Animals are supposed to be the same (same sex + same age, all coming from the same farm).  ...
written 5 months ago by SPbeginner0
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... 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 5 months ago by SPbeginner0
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... 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. ...
written 5 months ago by SPbeginner0 • updated 5 months ago by Aaron Lun21k
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... 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 5 months ago by SPbeginner0
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... So, for you, my code is correct ? I'll try to use splines for between-group comparison and let you know ! ...
written 6 months ago by SPbeginner0
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... 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 6 months ago by SPbeginner0
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... 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 6 months ago by SPbeginner0
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... 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 ...
written 6 months ago by SPbeginner0

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