User: hrishi27n

gravatar for hrishi27n
hrishi27n20
Reputation:
20
Status:
New User
Location:
Last seen:
3 months, 3 weeks ago
Joined:
2 years, 10 months ago
Email:
h********@gmail.com

Posts by hrishi27n

<prev • 38 results • page 1 of 4 • next >
0
votes
1
answer
139
views
1
answers
Comment: C: What is the best deseq2 design for this situtation?
... Thanks Micheal. I have roughly 140 patients. ...
written 4 months ago by hrishi27n20
3
votes
1
answer
139
views
1
answer
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 4 months ago by hrishi27n20 • updated 4 months ago by Michael Love25k
0
votes
1
answer
161
views
1
answers
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 4 months ago by hrishi27n20
1
vote
1
answer
161
views
1
answer
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 4 months ago by hrishi27n20 • updated 4 months ago by Michael Love25k
0
votes
1
answer
220
views
1
answers
Comment: C: Association analysis between gene expression and Phenotype
... Aaron, Thank you for your input. This is very helpful. ...
written 5 months ago by hrishi27n20
0
votes
1
answer
220
views
1
answers
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 5 months ago by hrishi27n20
5
votes
1
answer
220
views
1
answer
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 5 months ago by hrishi27n20 • updated 5 months ago by Aaron Lun24k
0
votes
1
answer
661
views
1
answers
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 21 months ago by hrishi27n20
0
votes
1
answer
661
views
1
answers
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 21 months ago by hrishi27n20
0
votes
1
answer
661
views
1
answers
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 21 months ago by hrishi27n20

Latest awards to hrishi27n

Popular Question 10 months ago, created a question with more than 1,000 views. For Clustering differential expression results from voomWithQualityWeights
Popular Question 10 months ago, created a question with more than 1,000 views. For Cell type specific cell markers for Seurat based analysis.
Popular Question 10 months ago, created a question with more than 1,000 views. For When is centering and scaling needed before doing hierarchical clustering?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 225 users visited in the last hour