User: hrishi27n

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hrishi27n0
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Posts by hrishi27n

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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 5 days ago by hrishi27n0 • updated 4 days ago by Michael Love14k
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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 3 months ago by hrishi27n0 • updated 3 months ago by Michael Love14k
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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 3 months ago by hrishi27n0 • updated 3 months ago by chris86330
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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 3 months ago by hrishi27n0 • updated 3 months ago by Michael Love14k
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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 4 months ago by hrishi27n0 • updated 4 months 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 7 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 7 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 7 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 7 months ago by hrishi27n0 • updated 7 months ago by James W. MacDonald45k
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Comment: C: Using voomWithQualityWeights for differential expression analysis.
... updated the code ...
written 7 months ago by hrishi27n0

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