User: hrishi27n

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hrishi27n0
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Posts by hrishi27n

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Cell type specific cell markers for Seurat based analysis.
... Hello All, This may sound like a vague question but your help and inputs on this could really help me move forward. I am helping a bench scientist with his single cell RNA sequencing data generated using drop-seq platform. Memory cells CCR7+/CD45RA-  were used for this experiment and were extracted ...
clustering single cell seurat written 11 days ago by hrishi27n0 • updated 11 days ago by ankur.chakravarthy.1010
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Comment: C: Regressing effect of treatment on RNA-seq expected count from rsem.
... James, thank you for responding.  My medication vector is something like below, after running removeBatchEffect it seems from the PCA that the medication effect is gone but the untreated points have also switched a little bit which I think should not have happened. Is there a way to prevent this fr ...
written 3 months ago by hrishi27n0
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Comment: C: Regressing effect of treatment on RNA-seq expected count from rsem.
... James, so I used both removeBatchEffect and ComBat separately to see what worked better for me, it seems that removeBatchEffect regressed most of the medication effect.  Just to be sure and to see if we can improve this, I am pasting my code snippet below.  For removeBatchEffect is it necessary to p ...
written 3 months ago by hrishi27n0
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Comment: C: Regressing effect of treatment on RNA-seq expected count from rsem.
... Thank you James.  ...
written 3 months ago by hrishi27n0
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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 3 months ago by hrishi27n0 • updated 3 months ago by James W. MacDonald43k
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Comment: C: Using voomWithQualityWeights for differential expression analysis.
... updated the code ...
written 3 months ago by hrishi27n0
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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 3 months ago by hrishi27n0
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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 3 months ago by hrishi27n0 • updated 3 months ago by Gordon Smyth30k
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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 5 months ago by hrishi27n0
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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 5 months ago by hrishi27n0 • updated 4 months ago by Yuan Tian70

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