User: LucyS

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LucyS0
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Posts by LucyS

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Comment: C: PANTHER and DAVID can't recognized some Ensembl gene ID?
... Thank you Guangchuang! This package is very useful! The only problem is I need to updated my R version:) ...
written 5 days ago by LucyS0
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PANTHER and DAVID can't recognized some Ensembl gene ID?
... Hi all, I am trying to do GO terms annotation using a set of interesting human genes(with Ensembl gene id) and background, they are from RNA-seq data. However, whether I using PANTHER or DAVID, there's always more than 20% gene ids can't be mapped and I want to save these unmapped ids. I have try us ...
gene rna-seq written 5 days ago by LucyS0 • updated 5 days ago by Guangchuang Yu1.6k
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batch effect of repeated experiment
... I have a transcriptomic dataset that has three batches, when PCA analysis, there is intra batch effect in batch 1. Therefore we repeated the experiment in three new batches, using the same samples but random their orders so they randomly allocated to the new batches. The result of the repeated exper ...
gene R rna-seq written 10 weeks ago by LucyS0 • updated 26 days ago by Biostar ♦♦ 20
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Answer: A: Gwas - Permutation Testing?
... hi Darren, a paper might help you:[enter link description here][1], it explains how FDR in permutation calculate:) [1]: https://academic.oup.com/bioinformatics/article/21/23/4280/194680/A-note-on-using-permutation-based-false-discovery ...
written 7 months ago by LucyS0
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How to Calculate FDR in permutation F test
... Hi all, I am a little confused about how to calculate FDR after permutation F test. Assume there is 6000 genes in my data. And for each gene, I perform 1000 permutation F test and got 1000 F value, which includes 1 original F value and 999 permutating F value. And p-value = sum(F > F-original) ...
R written 8 months ago by LucyS0 • updated 7 months ago by Jean-Karim Heriche13k
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Comment: C: remove effect of factors in differential analysis
... thanks! I have re-edit it and hope it's more clear now! ...
written 8 months ago by LucyS0
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remove effect of factors in differential analysis
... Assume there's two factors that affect the metabolite compounds content of my data: Factor A and Factor B, Factor Ahas three level and Factor B has two level, so there is 3*2 groups, and all in one experiment batch. I only want to get the compounds related to the Factor A, however Factor B seems t ...
R written 8 months ago by LucyS0
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Comment: C: remove batch effect for multiple tumor data
... thanks for your answer b.nota! ...
written 8 months ago by LucyS0
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Comment: C: remove batch effect for multiple tumor data
... Hi b.nota. Thanks for your suggestions! I modified my post, hope it's more clear now! My main aim now is to find differentially expressed genes of one tissue, and then see if it intersects with the other tissue's result! ...
written 8 months ago by LucyS0
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remove batch effect for multiple tumor data
... Dear all, I am dealing with a data contains samples with 7 tissues(normal control vs. tumor), and 2 experimental batches. These control and tumor of one tissue is not evenly distributed in two batches. For one specific tissue, there are 3~4 control samples, 3~4 tumor samples. The main aim of this ...
multiple samples rna-seq batch effect written 8 months ago by LucyS0

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