User: hrishi27n

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hrishi27n0
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Posts by hrishi27n

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Comment: C: DESeq: Question about contrast and group-wise subsetting.
... You are right it was indeed the subsetting. The plot now shows a straight line. Thank you very much Micheal.  Here is the plot: https://i.imgur.com/1sXmMYZ.png ...
written 6 months ago by hrishi27n0
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Comment: C: DESeq: Question about contrast and group-wise subsetting.
... Micheal, I have attached the plot below.  This is my overall code to generate the plot:  (My data has technical replicates which I have collapsed together) Instead of using the padj I have used pval to generate the plot, most my padj value where 0.99 for the RP : 200nm vs 50nm comparison.  libr ...
written 6 months ago by hrishi27n0
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Comment: C: DESeq: Question about contrast and group-wise subsetting.
... Micheal, thank you for your response. I am uploading a PCA plot of my full data below. You can clearly see from the PCA that the condition "None" (untreated) is clearly separating regardless of the disease category. I tried investigating how the results looked when all samples were used in the model ...
written 6 months ago by hrishi27n0
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Comment: C: Appropriate DESeq2 design for multi-factor comparison within group?
... Thanks Micheal. I really appreciate your help.  ...
written 6 months ago by hrishi27n0
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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 6 months ago by hrishi27n0
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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 7 months ago by hrishi27n0 • updated 7 months ago by Michael Love18k
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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 10 months ago by hrishi27n0 • updated 10 months ago by Michael Love18k
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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 10 months ago by hrishi27n0 • updated 10 months 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 10 months ago by hrishi27n0 • updated 10 months ago by Michael Love18k
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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 months ago by hrishi27n0 • updated 11 months ago by ankur.chakravarthy.1010

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