User: sidreed34

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sidreed340
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Posts by sidreed34

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Comment: C: One-way hypothesis test in limma
... So if one wanted to implement one-sided tests (LFC > LT and LFC < -LT seperately), with an lfc threshold of LT, would the code look like this? ``` # testing LFC > 0 (condition1 > condition2 for the given contrast, same code as the original post) lfc <- log2(2)#arbitrary lfc threshold ...
written 7 weeks ago by sidreed340
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Comment: C: scale_counts targetSize normalization for recount2 counts
... Thank you very much, this helps clarify a lot for me. For question 2 a better way to phrase it would have been "Why specifically would running scale_counts() and read_counts() return nonsensical results?" ...
written 3 months ago by sidreed340
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Comment: C: scale_counts targetSize normalization for recount2 counts
... Hello, Thank you for your response, however I am still confused about some things. 1. When you say scaling to the same AUC, do you mean dividing each sample column by it's AUC value, to account for coverage differences between samples? 2. Is accounting for coverage *and* mapped reads redundant ( ...
written 3 months ago by sidreed340
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scale_counts targetSize normalization for recount2 counts
... I am currently trying to conduct a differential expression analysis using the recount data. I want to compare the GTEx and TCGA data against a specific set of separate runs I have picked out. My issue is with the targetSize argument in the scale_counts function. By default it is set 4e7 for all run ...
recount written 4 months ago by sidreed340 • updated 3 months ago by Leonardo Collado Torres690

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