User: hrishi27n

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hrishi27n20
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Posts by hrishi27n

<prev • 38 results • page 3 of 4 • next >
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Regressing effect of treatment on RNA-seq expected count from rsem.
... Hello All, I have RNA-seq data collected by sequencing around 30 individuals(similar phenotypes) and my goal is to  group/cluster these patients based upon their expected counts obtained from rsem.  Most of these patients are on a few different medications and some are untreated, my PCA shows a cle ...
rna bioinformatics rna-seq science written 2.4 years ago by hrishi27n20 • updated 2.4 years ago by James W. MacDonald51k
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Comment: C: Using voomWithQualityWeights for differential expression analysis.
... updated the code ...
written 2.4 years ago by hrishi27n20
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Comment: C: Using voomWithQualityWeights for differential expression analysis.
... Gordon thank you very much for your response. I would like to cluster the samples by using just the differentially expressed genes(I tried using all genes but saw no clusters). I tried doing PCA, hierarchal clustering and even MDS plots on the samples using the rsem values but don't really see to se ...
written 2.4 years ago by hrishi27n20
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Clustering differential expression results from voomWithQualityWeights
... Hello all, I am very new to RNA-seq analysis and have a very specific question about using voomWithQualityWeights For my analysis, I am using the expected counts generated from rsem tool to run my differential expression analysis.  I am using edgeR for TMM normalization and then voomWithQualityWe ...
limma edger rna rsem written 2.4 years ago by hrishi27n20 • updated 2.4 years ago by Gordon Smyth38k
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Comment: C: sc-RNA data analysis using scater
... Aaron, Thanks for the reply. My "read count" file does't include the ERCC's. A grep for "^ERCC-" doesn't really give anything, however the ERCC's are provided in a separate file. I guess I might have to do a rbind on the gene count file to include the spike-in data.  ...
written 2.6 years ago by hrishi27n20
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champ.load getting filtered RGChannelSet
... Hello, I am using champ.load to filter my probes from my IDAT files. I understand the champ.load function returns mset,rgset,pd,beta etc. I see that the mset includes the filtered features(everything left after det P,dropSNP,dropXY), but the rgset is unchanged, I have pasted a section of the output ...
champ methylation written 2.6 years ago by hrishi27n20 • updated 2.5 years ago by Yuan Tian80
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sc-RNA data analysis using scater
... Hello All, I am trying to analyze data for a single cell RNA sequencing experiment, for QC and normalization I am considering using the scater package. There are a few things I would like to know before starting analyzing this dataset. All your help and suggestions are much appreciated. This is my ...
scater scrna written 2.6 years ago by hrishi27n20 • updated 2.6 years ago by Aaron Lun24k
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Comment: C: Scran normalization error with computeSumFactors
... Thanks for the reply Aaron. I will try reducing the pool sizes, you are also right that I need an aggressive filtering strategy. I will add something like below to ensure that lowly expressed genes are removed.   keep_feature <- rowMeans(counts(ScaterObject)) >= 5 ...
written 2.6 years ago by hrishi27n20
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Scran normalization error with computeSumFactors
... Hello All, I am trying to analyze sc-RNA data using both scater and scran. While trying to run normalization using scran via the computeSumFactors method, I get the following error. Could someone please explain me what this error means and if there a way to fix it? Appreciate all your help and sugg ...
scran scater written 2.6 years ago by hrishi27n20 • updated 2.6 years ago by Aaron Lun24k
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Answer: A: Error using Bumphunter and Block finder using CHAMP
... Thanks for replying.  You are right about the message with "0 clusters", I was using only 10 CpG's for my test run, using all CpG's solved the problem. ...
written 2.8 years ago by hrishi27n20

Latest awards to hrishi27n

Popular Question 10 months ago, created a question with more than 1,000 views. For Clustering differential expression results from voomWithQualityWeights
Popular Question 10 months ago, created a question with more than 1,000 views. For Cell type specific cell markers for Seurat based analysis.
Popular Question 10 months ago, created a question with more than 1,000 views. For When is centering and scaling needed before doing hierarchical clustering?

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