User: xfwang

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xfwang20
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United States
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3 years, 4 months ago
Joined:
4 years, 10 months ago
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x*****@ku.edu

Posts by xfwang

<prev • 19 results • page 2 of 2 • next >
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Comment: C: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... Sorry, there is a type  log2(BEH_Nor_mean/FIN_Nor_mean) should be  log2(VEH_Nor_mean/FIN_Nor_mean) ...
written 4.8 years ago by xfwang20
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Comment: C: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... I don't know how to upload an image. If the contents of the table do not make sense, please let me know. ...
written 4.8 years ago by xfwang20
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Answer: A: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... Dear Michael, I sorry I am still struggling about the different results between DESeq2 and Cuffdiff. Here is a new question about how DESeq2 calculate log2FoldChange? The columns "FIN_Nor_mean" and "VEH_Nor_mean" are got from DESeq2 by code "PFC_dds_countsNor <- counts(PFC_dds, normalized=TRUE) ...
written 4.8 years ago by xfwang20
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Comment: C: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... "There's no extra column which is a flag. We chose not to add additional columns to the results table because the information is contained in the values for baseMean, pvalue and padj. The logic is described in the vignette (it sounds like you've seen this already). " Actually, I don't see there is ...
written 4.8 years ago by xfwang20
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Comment: C: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... So, my understanding is that if we have multiple levels (>2) for a factor, it is similar to this test (H0: ß1=ß2=0 VS H1: at least one of ß1 and ß2 is not 0) when we want to test significance for a main effect. That is why I think I need to change the default Wald test to LRT when I have a factor ...
written 4.8 years ago by xfwang20
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Comment: C: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... I double check my notes for Categorical Analysis which is a class for statistics. I see that Wald test is not for multiple parameters. For example, H0: ß1=ß2=0 H1: at least one of ß1 and ß2 is not 0, then Wald test is not for this testing because wald test is not for multiple parameters. Anyway, ...
written 4.8 years ago by xfwang20
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Answer: A: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... Here are some new questions: First, as I said I did pairwise comparisons on my first and second dataset (there is only one factor with 2 levels for each of them), and the results from Cuffdiff and DESeq2 are so different. I think I found the reason for this big difference. The majority of DEG detec ...
written 4.8 years ago by xfwang20
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Comment: C: A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
... Hi Michael, Thank you so much for responses to my questions so quickly! Actually, I read the vignette again and did more research for this project. But, I still have some questions in my mind about DESeq2 (I will 'Add comment' for clarifications here and also ask some new questions).  "This is not ...
written 4.8 years ago by xfwang20
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A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
...     Dear DESeq2 community, I am trying to use DESeq2 to detect DEG for my RNAseq data because it can deal with multi-factor designs, although there is not only multi-factor analysis in my experiment data. Let me clarify my datasets firstly. For my first and second dataset, there is only one fact ...
deseq2 written 4.8 years ago by xfwang20

Latest awards to xfwang

Popular Question 3.4 years ago, created a question with more than 1,000 views. For A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2
Popular Question 4.0 years ago, created a question with more than 1,000 views. For A couple of questions about baseMean, RPKM, and multi-factor analysis for DESeq2

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