User: mahes.muniandy

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Posts by mahes.muniandy

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Job: Postdoc/Bioinformatician: Helsinki - Obesity Research Unit, University of Helsinki
... The research group of Prof. Kirsi Pietiläinen at the Obesity Research Unit, University of Helsinki, located at Biomedicum Helsinki, is looking for a Postdoctoral Scientist. The translational lab Pietiläinen is focused on global metabolic profiling of obesity by systems biology methods, transcripto ...
job multiomics single-cell rna written 28 days ago by mahes.muniandy0
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Comment: C: Time course experiment using limma with voom
... Hi Aaron, Thank you once again. I have tried the below model as suggested and as expected I get fewer significant genes compared to not having the time points in the model. design <- model.matrix(~ 0 + patient + time + time:wloss) Just one more question, if I want to find the effects of ag ...
written 4 months ago by mahes.muniandy0
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Comment: C: Time course experiment using limma with voom
... Hi Aaron, Thank you so much for the guidance. Yes, some individuals lose more weight than others and weight loss is not linear with respect to time, plus between timepoints 2 and 3, the diet is different than between timepoints 1 and 2. I realise all this complicates matters and I am quite confused ...
written 4 months ago by mahes.muniandy0
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Time course experiment using limma with voom
... Hi, I am performing RNA sequencing data analysis on weight loss data with three timepoints: before diet, 2 months after diet and 10 months after diet (I’m calling the timepoints TP1, TP2, TP3). My variable of interest is percentage weight lost, so I set my percentage weight lost at TP1 at 0 and TP2 ...
limma voom rna seq time-course experiments written 4 months ago by mahes.muniandy0 • updated 4 months ago by Aaron Lun25k
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limma for metabolite data
... Hello, My name is Mahes Muniandy and I am a doctoral student working on twin data. I have used limma previously for gene expression as well as methylation data and would now like to use it on my metabolomics data - to detect within twin-pair differences. I have two quesions: 1) Since metabolite d ...
metabolomics limma limma paired analysis written 2.6 years ago by mahes.muniandy0 • updated 2.6 years ago by Aaron Lun25k
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Comment: C: contrast matrix to compare 3 groups in limma
... Dear Aaron, This now works well, thank you for your help. Mahes ...
written 3.8 years ago by mahes.muniandy0
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contrast matrix to compare 3 groups in limma
... Hi, My name is Mahes Muniandy and I am a doctoral student working on twin data. I have gene expression (Affymetrix HGU133 plus 2) data for monozygotic twins discordant for obesity. I clustered my gene expression data using heavy/lean ratios for each twin pair and obtained 3 groups and would like to ...
limma written 3.8 years ago by mahes.muniandy0 • updated 3.8 years ago by Aaron Lun25k
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Twin analysis using limma
... Hello, My name is Mahes Muniandy and I am a doctoral student working on twin data.  I would like to compare the gene expression (Affymetrix HGU133 plus 2) between lean and obese people and see how sex (Male/Female) affects the gene expression. So, I would like to do within twin-pair differences (26 ...
limma limma paired analysis written 3.9 years ago by mahes.muniandy0 • updated 3.9 years ago by Aaron Lun25k
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How many probesets/genes can WGCNA handle?
... Hi, My name is Mahes Muniandy and I'm a phd student at the University of Helsinki. I have a question about WGCNA - I have around 50,000 probesets after normalization. I filtered out the ones with low variance across my samples and still end up with about 30,000. Is this still too many for clusterin ...
wgcna written 4.1 years ago by mahes.muniandy0
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WGCNA package with monozygotic twin data
... Hello, My name is Mahes Muniandy and I am a doctoral student working on twin data.  I have been using the WGCNA package to cluster and analyse my traits and gene expression data. Because I am using monozygotic twin data and would like to see how my twins cluster as pairs, I have taken the ratios of ...
wgcna paired within-pair analysis twin analysis written 4.5 years ago by mahes.muniandy0 • updated 4.5 years ago by Peter Langfelder2.3k

Latest awards to mahes.muniandy

Popular Question 2.6 years ago, created a question with more than 1,000 views. For contrast matrix to compare 3 groups in limma
Popular Question 2.6 years ago, created a question with more than 1,000 views. For limma for metabolite data

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