User: solgakar@bi.technion.ac.il

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Posts by solgakar@bi.technion.ac.il

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Comment: C: Understanding differences in results with and without setting of pairing factor
... Thank you very much for all your help! I ran it with the MAP estimator, I will look into the results more deeply, but from a quick look these genes that we were discussing indeed look more similar to the results without the pairing factor. ...
written 19 months ago by solgakar@bi.technion.ac.il60
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Comment: C: Understanding differences in results with and without setting of pairing factor
... Another note: When comparing type 1 samples (with lower library size) to type 3 samples (with higher library size) I see the same results (padj = 0.87) for these genes as in the comparison presented above (type 1 vs. type 2). Olga ...
written 19 months ago by solgakar@bi.technion.ac.il60
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Comment: C: Understanding differences in results with and without setting of pairing factor
... The library sizes (# counted reads) do differ more than I usually see: Sample Cell type Library size + size factor 1 type1 2.5M  + 0.49 2 type1 5.5M + 1.03 3 type2 4M + 0.68 4 type2 3.5M  + 0.64 5 type3 10M  + ...
written 19 months ago by solgakar@bi.technion.ac.il60
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Comment: C: Understanding differences in results with and without setting of pairing factor
... Hi Michael, Here are 4 examples for such genes: Sample CellType Mice gene 1 gene 2 gene 3 gene 4 1 type1 m1 114.38 75.57 83.74 0 2 type1 m2 82.07 97.52 139.04 0 3 type2 m1 0 0 0 82.27 ...
written 19 months ago by solgakar@bi.technion.ac.il60
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Comment: C: Understanding differences in results with and without setting of pairing factor
... I have tried running DESeq() with betaPrior=FALSE, in some cases it indeed changed the statistical results but still in the cases where a gene is specifically expressed in a single cell type - the log2FoldChange is extremely high but both the p-value and adjusted p-value are very far from being sign ...
written 20 months ago by solgakar@bi.technion.ac.il60
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Comment: C: Understanding differences in results with and without setting of pairing factor
... This was also our primary thought. But still we are worried about these cases that I have presented above since it seems that this way we 'miss' the interesting cases of genes specific to a single cell type - which is one of the goals of the experiment. ...
written 20 months ago by solgakar@bi.technion.ac.il60
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Comment: C: Understanding differences in results with and without setting of pairing factor
... Hi Michael, First of all thank you very much for the response. Regarding the explanation of the second case, I can see the reason for that. But for the first case I still can't seem to understand why a whole set of genes having the same overall pattern of being expressed only in one cell type (in ...
written 20 months ago by solgakar@bi.technion.ac.il60
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Understanding differences in results with and without setting of pairing factor
... Hello, I am working on a RNA-Seq experiment in which there are 3 different cell types analyzed. For each cell type I have 2 biological replicates - each represent a different pool of mice. I first ran DESeq2 without setting the 'Mice' factor, meaning without pairing the 3 cell types of the same mi ...
deseq2 rna-seq paired samples written 20 months ago by solgakar@bi.technion.ac.il60 • updated 20 months ago by Michael Love20k
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Comment: C: how to deal the effect of enormous gene expression?
... Hi Michael, I am working with Maor on this project, first of all thank you very much for the reply. We have already spoken with the researcher that performed the experiment, What we are afraid of is that the high expression of the heat-shock response genes will cause a global decrease in the express ...
written 2.8 years ago by solgakar@bi.technion.ac.il60
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Comment: C: interpreting LRT results DESeq2
... As always, thank you very much for your quick reply! I am sorry to bother you with questions that are already answered in the help section, I don't know how I've missed it. ...
written 3.7 years ago by solgakar@bi.technion.ac.il60

Latest awards to solgakar@bi.technion.ac.il

Popular Question 2.8 years ago, created a question with more than 1,000 views. For Normalization in DESeq2
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Normalization in DESeq2
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Analyzing RNA-Seq data without replicates using DESeq

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