User: pennakiza

gravatar for pennakiza
pennakiza60
Reputation:
60
Status:
Trusted
Location:
Last seen:
2 days, 17 hours ago
Joined:
3 years, 10 months ago
Email:
b*******@hotmail.com

Posts by pennakiza

<prev • 37 results • page 1 of 4 • next >
3
votes
1
answer
204
views
1
answer
Filtering low variance genes for WGCNA
... Hello everyone, I have a question re filtering for low variance prior to WGCNA. I have got RNASeq data, pre-filtered for low counts and transformed with DESeq2 vst. I was wondering if you could help me select from the two methods below the one that is more correct for my data. filter <- fun ...
wgcna iqr variance filtering genefilter written 4 weeks ago by pennakiza60 • updated 4 weeks ago by Kevin Blighe69k
0
votes
1
answer
897
views
1
answers
Comment: A: WGCNA and SC-RNA Seq data
... Hi Kevin, I have filtered my dataset for low counts, so I have ended up with ~850 genes, and WGCNA runs quite smoothly but the module-trait correlations that I see are quite weak. I was wondering if that is because I am working with so few genes or because all those cells come from only 4 patient ...
written 8 months ago by pennakiza60
1
vote
1
answer
897
views
1
answer
WGCNA and SC-RNA Seq data
... Hello, I have a dataset of single-cell expression data (at the moment working on CD4 cells only) from 4 patients. Would 4 patients be enough to get any significant results, considering that my sample number is essentially 1200 cells? Thank you in advance! ...
sc-rna seq rna-seq wgcna written 8 months ago by pennakiza60
0
votes
1
answer
315
views
1
answers
Comment: C: Standard GSEA and RNA-seq data
... I might be completely wrong here but if I understand it correctly for the pre-ranked test one just loads a list of genes ranked by the shrunken log2 fold change values, along with those values. Is that wrong? Excuse my ignorance please! Thanks, Penny ...
written 10 months ago by pennakiza60
0
votes
1
answer
315
views
1
answers
Comment: C: Standard GSEA and RNA-seq data
... Thanks Kevin, Yes, I am referring to the program "GSEA" by the Broad Institute. When you say you would use the DESeq2 vst you mean the table of transformed counts to do a standard GSEA, instead of the Pre-Ranked GSEA? Sorry for my confusion! -Penny ...
written 10 months ago by pennakiza60
0
votes
1
answer
315
views
1
answer
Standard GSEA and RNA-seq data
... Hi all, I am a bit confused with GSEA and I was hoping that you could help me. I've got RNA-Seq data (two conditions with 5 replicates each). The GSEA website says that the suggested method is the standard one vs the pre-ranked so I decided to give it a try. I have read the following on [this][1] ...
gsea rna-seq written 11 months ago by pennakiza60 • updated 11 months ago by Kevin Blighe69k
0
votes
2
answers
714
views
2
answers
Comment: C: RNA Seq data with GSEA
... That's cool, in this case I am getting the same results, which is reassuring! Thank you very much for your help! ...
written 12 months ago by pennakiza60
0
votes
2
answers
714
views
2
answers
Comment: C: RNA Seq data with GSEA
... Thank you very much! I thought that you needed to transform the data before but I will certainly try it without it. I have tried to used preranked but in some cases I have only a few DE genes (p-adj <0.05) and if I only use those I don't get any gene sets enriched. ...
written 12 months ago by pennakiza60
0
votes
2
answers
714
views
2
answers
Comment: C: RNA Seq data with GSEA
... Thank you Gordon! I will try camera too! ...
written 12 months ago by pennakiza60
2
votes
2
answers
714
views
2
answers
RNA Seq data with GSEA
... Hi all, I am a bit confused with how I should be transforming my data to use it with GSEA. I have tried two different approaches and I am not sure which one is the best. First, I have created a DGElist, filtered my low count reads and transformed it with voom. These data I fed then to GSEA. y ...
voom vsn rna-seq gsea written 12 months ago by pennakiza60 • updated 12 months ago by Gordon Smyth2.1k

Latest awards to pennakiza

Popular Question 2.0 years ago, created a question with more than 1,000 views. For DESeq2 object problem with padj

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2383 users visited in the last hour
_