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User: dhibar

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dhibar50
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1 year, 10 months ago
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Posts by dhibar

<prev • 5 results • page 1 of 1 • next >
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DESeq2 and fdrtool: applying FDR correction when the empirical sigma is greater than 1
... Hello, I am following the guide found here (http://www-huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html) to estimate differential gene expression in my two-condition RNAseq dataset. When I look at my histogram of observed p-value statistics I end up with a plot like this: dds <-  nbinom ...
deseq2 fdrtool written 2.7 years ago by dhibar50 • updated 2.7 years ago by Bernd Klaus530
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Comment: C: High number of significant DE genes with low baseMean, is this abnormal?
... Thanks Michael and Ryan. The normalized counts for the top DE gene looks like several of the subjects have a count=0 so I'm wondering if the NB model used in DESeq2 provides accurate estimates in cases like that. I wonder too about the biological significance, if it is significantly DE in the model ...
written 2.8 years ago by dhibar50
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High number of significant DE genes with low baseMean, is this abnormal?
... I have a relatively large RNAseq data set: 360 Human blood biological replicates, 100bp PE reads with 60M read depth on average, with Poly-A removal. I'm analyzing these data with DESeq2 following these basic steps: dds = DESeqDataSetFromMatrix(countData = dat0, colData = colDat, design = ~ Age + ...
deseq2 written 2.8 years ago by dhibar50 • updated 2.8 years ago by Ryan C. Thompson7.2k
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Comment: C: Possible to incorporate the sign or direction of an effect in the IHW covariate?
... Thanks, this seems to be exactly what I am looking for! ...
written 2.9 years ago by dhibar50
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Possible to incorporate the sign or direction of an effect in the IHW covariate?
... I am wondering if it is possible to incorporate information about the direction of an effect in the test distribution into a covariate used in IHW? More specifically, I have a set of DESeq2 results: P-values and Beta statistics for my predictor of interest. Separately I obtained DESeq2 results from ...
ihw written 2.9 years ago by dhibar50 • updated 2.9 years ago by Nikos Ignatiadis160

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Student 22 months ago, asked a question with at least 3 up-votes. For Possible to incorporate the sign or direction of an effect in the IHW covariate?

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