User: hrishi27n

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hrishi27n20
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Posts by hrishi27n

<prev • 38 results • page 1 of 4 • next >
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Comment: C: What is the best deseq2 design for this situtation?
... Thanks Micheal. I have roughly 140 patients. ...
written 10 weeks ago by hrishi27n20
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What is the best deseq2 design for this situtation?
... I am working on analyzing a dataset using DESeq2. The main goal of the analysis is to compare the gene expression profiles between treated and untreated group. Since we also have sex information on the patient, we are also looking at sex-specific differences of the main condition(Treatment). I have ...
deseq2 written 10 weeks ago by hrishi27n20 • updated 10 weeks ago by Michael Love24k
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Comment: C: Extracting sex specific differences between groups using DESeq2 interactions?
... Micheal thanks for the reply. I read the results section and now things are a little more clear. So I ended up combining groups into a single factor. Gr <- factor(paste0(Pheno$Condition,Pheno$Sex)) dds <- DESeqDataSetFromMatrix(countData = myFile, colData = Pheno, design= ~Gr+Age) ...
written 12 weeks ago by hrishi27n20
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Extracting sex specific differences between groups using DESeq2 interactions?
... Hello, I am very new to using interactions using DESeq2 and handling multi-factor design. I have two groups 'Treated' and 'Untreated' which include both males and females in both groups. First, I am interested in looking into comparing treated vs untreated without considering sex specific effects. ...
deseq2 written 12 weeks ago by hrishi27n20 • updated 12 weeks ago by Michael Love24k
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Comment: C: Association analysis between gene expression and Phenotype
... Aaron, Thank you for your input. This is very helpful. ...
written 3 months ago by hrishi27n20
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Comment: C: Association analysis between gene expression and Phenotype
... Aaron, thank you for responding to my post. I have updated the post to include more info and code. Appreciate all your help and comments. ...
written 3 months ago by hrishi27n20
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Association analysis between gene expression and Phenotype
... Hello All, I have RNA data generated using the smart-seq2 protocol and I am interested in running association analysis (some thing like logistic regression but with limma) between the gene expression values and cohort status. I have quantified the transcripts as TPM using RSEM. I am considering nor ...
limma rna singlecell written 3 months ago by hrishi27n20 • updated 3 months ago by Aaron Lun24k
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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 19 months ago by hrishi27n20
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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 19 months ago by hrishi27n20
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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 19 months ago by hrishi27n20

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