User: hrishi27n

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hrishi27n20
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Posts by hrishi27n

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Comment: C: Appropriate DESeq2 design for multi-factor comparison within group?
... Thanks Micheal. I really appreciate your help.  ...
written 21 months ago by hrishi27n20
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DESeq: Question about contrast and group-wise subsetting.
... Hello All, I am performing a DEG analysis using DESeq2 and would really appreciate your advice on the results(contrast) section of my analysis.  I have 5 disease categories(RM, RP, SP_progress, SP_stable and healthy) for each category we extracted monocytes and treated these monocytes with differe ...
deseq deseq2 written 21 months ago by hrishi27n20
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Appropriate DESeq2 design for multi-factor comparison within group?
... Hello All, I am trying to run DE analysis using DESeq2 and wanted to know what would be a better/correct design matrix for my analysis. I have two disease condition A and B. Cells(CD4) from patient groups A and B were treated with different concentration of a certain chemical. The concentrations ar ...
deseq deseq2 written 21 months ago by hrishi27n20 • updated 21 months ago by Michael Love25k
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Time series comparison with DESEQ2
... Hello All, For my analysis I have three time points Time1, Time2 and Time3 these were measured based upon three different treatments. I am trying to run differential analysis between T1 vs T2, T1 vs T3 and T2 vs T3, I have some technical replicates that I summed using the collapseReplicates() funct ...
rnaseq deseq2 rna written 2.0 years ago by hrishi27n20 • updated 2.0 years ago by Michael Love25k
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When is centering and scaling needed before doing hierarchical clustering?
... Hello All, I am working on a clustering project where we have collected protein data from over 100 patients samples. This data is normalized and log transformed to achieve a uniform distribution. The goal is to cluster samples based upon their similarities, I am using hierarchal clustering and tryi ...
clustering hierarchical clustering written 2.0 years ago by hrishi27n20 • updated 2.0 years ago by chris86380
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RNA sequencing analysis for time point experiment using DeSeq2
... I have the following two questions, I would highly appreciate your input on both of these. 1) How to create a design matrix for a time point comparison where the patients were on and off treatment using DeSeq2? The patients were initially on drugA for a month and then off drugA for another month, t ...
rnaseq deseq2 rna written 2.1 years ago by hrishi27n20 • updated 2.1 years ago by Michael Love25k
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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 2.1 years ago by hrishi27n20 • updated 2.1 years ago by ankur.chakravarthy.1040
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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 2.3 years ago by hrishi27n20
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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 2.3 years ago by hrishi27n20
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Comment: C: Regressing effect of treatment on RNA-seq expected count from rsem.
... Thank you James.  ...
written 2.3 years ago by hrishi27n20

Latest awards to hrishi27n

Popular Question 9 months ago, created a question with more than 1,000 views. For Clustering differential expression results from voomWithQualityWeights
Popular Question 9 months ago, created a question with more than 1,000 views. For Cell type specific cell markers for Seurat based analysis.
Popular Question 9 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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