User: Rahil

gravatar for Rahil
Rahil170
Reputation:
170
Status:
Trusted
Location:
Last seen:
46 minutes ago
Joined:
3 years, 10 months ago
Email:
r**************@yahoo.com

Posts by Rahil

<prev • 103 results • page 1 of 11 • next >
0
votes
0
answers
75
views
0
answers
Finding a gene signature among multiple group
... Hi all, I have a expression profile (RNAseq) of 580 immune-related genes for 350 samples that are already classified into 4 subtypes. I want to find the genes (out 0f 580) that significantly have different expression among these 4 subtypes. In an article Significance analysis of microarrays (SAM) m ...
rnaseq signature sam written 3 days ago by Rahil170
0
votes
0
answers
123
views
0
answers
Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
... Thanks rpolicastro! Oh yes that makes more sense. Is there any package for doing this in r? ...
written 13 days ago by Rahil170
0
votes
0
answers
123
views
0
answers
Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
... What about getting average instead? Is there any r package that can do this? ...
written 13 days ago by Rahil170
0
votes
0
answers
123
views
0
answers
Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
... I got from someone as she said this is FPKM data from Cufflinks pipeline. ...
written 13 days ago by Rahil170
4
votes
0
answers
123
views
0
answers
how to get ride of duplicated genes when we also have duplicated Ensemble ID in the expression profile?
... Hi all, I have a mouse expression profile that is annotated with gene symbols and many of them are duplicated. I usually use collapseRows function with maxMean method from WGCNA package to get ride of duplicated genes. However, this time I realized that there are also some duplication in ENSEMBLE I ...
collapserows duplicated ensemble id rna-seq written 13 days ago by Rahil170
0
votes
1
answer
163
views
1
answers
Comment: C: Batch correction using DESeq2
... Yes, solved! Thanks! ...
written 11 weeks ago by Rahil170
0
votes
1
answer
1.6k
views
1
answers
Comment: C: Batch correction in DESeq2
... Thanks @Kevin, I do like your way of clarifying issues! I appreciate if you answer my question. I don't want to do differential expression analysis, I just want to normalize my RNAseq data and then do some clustering and classification .. Based on your explanation I realized after adding the batch i ...
written 11 weeks ago by Rahil170
0
votes
1
answer
163
views
1
answers
Comment: C: Batch correction for one condition in DESeq2
... Oh, the second line of my script was left, sorry. I edited my post. Thanks! ...
written 11 weeks ago by Rahil170
0
votes
1
answer
163
views
1
answers
Comment: C: Batch correction for one condition in DESeq2
... If I ignore that date, is it correct to add only genotype to the design formula to account for its effect? This script is correct for normalizing the data? dds <- DESeqDataSetFromMatrix(as.matrix(all), colData, design = ~ Genotype) vsd <- vst(dds, blind = F) assay(vsd) I really ...
written 11 weeks ago by Rahil170
0
votes
1
answer
163
views
1
answers
Comment: C: Batch correction for one condition in DESeq2
... Many thanks swbarnes for your prompt reply! Yes, they are all primary tumors but with different genotypes. Sorry I don't get your question. I named the headers. What they should be? ...
written 11 weeks ago by Rahil170

Latest awards to Rahil

Centurion 13 days ago, created 100 posts.
Appreciated 10 weeks ago, created a post with more than 5 votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Calling CNV using bcftools
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 4 months ago, created a question with more than 1,000 views. For Downstream analysis of VCF files obtained from VarScan2
Popular Question 4 months ago, created a question with more than 1,000 views. For Downstream analysis of VCF files obtained from VarScan2
Popular Question 6 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 11 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Supporter 12 months ago, voted at least 25 times.
Popular Question 19 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Student 22 months ago, asked a question with at least 3 up-votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1638 users visited in the last hour