User: pennakiza

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pennakiza50
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Posts by pennakiza

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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 13 days ago by pennakiza50
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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 13 days ago by pennakiza50
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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 3 months ago by pennakiza50
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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 3 months ago by pennakiza50
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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 3 months ago by pennakiza50 • updated 3 months ago by Kevin Blighe60k
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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 4 months ago by pennakiza50
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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 4 months ago by pennakiza50
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Comment: C: RNA Seq data with GSEA
... Thank you Gordon! I will try camera too! ...
written 4 months ago by pennakiza50
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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 4 months ago by pennakiza50 • updated 4 months ago by Gordon Smyth1.6k
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Decontaminate RNASeq data from other cell types?
... Hello all, Very ambitious question coming! So I have RNA Seq data from CD4+ cells, which are selected using a kit. However I used CIBERSORT on them and I see that there is a significant contamination with other immune cell types, mainly B and NK cells. I was wondering if there is any way to extract ...
gene expression rna seq decontamination written 4 months ago by pennakiza50

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Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2 object problem with padj

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