User: mousheng xu

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mousheng xu10
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Posts by mousheng xu

<prev • 20 results • page 1 of 2 • next >
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How to install a bioconductor package RMySQL and specify R parameters
... I am trying to install CopywriteR, which failed at updating a dependent package RMySQL. The error I got was as follows: ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libmysqlclient was not found. Try installing:  * deb: libmariadb-client-lgpl-de ...
software error R written 20 days ago by mousheng xu10 • updated 19 days ago by shepherl ♦♦ 510
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Comment: C: edgeR and Normalization of RNAseq data using ERCC controls
... How to compute ERCC normalized library sizes for your own samples? Can edgeR do this? Thank you. ...
written 7 months ago by mousheng xu10
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Comment: C: edgeR glmLRT with test="F"?
... The edgeR user's guide states: "While the likelihood ratio test is a more obvious choice for inferences with GLMs, the QL F-test is preferred as it reflects the uncertainty in estimating the dispersion for each gene. It provides more robust and reliable error rate control when the number of replica ...
written 7 months ago by mousheng xu10
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Comment: C: edgeR glmLRT with test="F"?
... Thanks much for the reply. How about the type II error of QLF vs LRT? Also, why replicates have anything to do with the choice of QLF/LRT? Does QLF take into account of within group variation (as revealed by the replicates) while LRT does not? ...
written 7 months ago by mousheng xu10
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Comment: C: edgeR glmLRT with test="F"?
...   Read the paper you mentioned before. ERCC is meant to reduce the variance generated during PCR amplification and library preparation, so it should have its merit. I am not saying we should use ERCC to replace other normalization methods like the one used in edgeR. Our experience with ERCC normali ...
written 7 months ago by mousheng xu10
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Comment: C: edgeR glmLRT with test="F"?
... I just noticed something that you guys might feel interesting, although I am not sure if it is true: if you have done ERCC normalization, even with replicates, LRT might be a better choice.  The reason I am saying this is that I have ERCC normalized samples, fed into RSEM, and then to edgeR. The p- ...
written 7 months ago by mousheng xu10
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Comment: C: [edgeR Usage] Constructing DGE test with fewer input variables
... You are great! So helpful! 1. Need to digest the difference of glm & lm. Thought they were almost identical except that glm allows "link"; 2. OK, makes sense. So if you have enough replicates (e.g. 4 replicates each for 0, 0.1, 0.5, 1mM concentration for disease samples and normal samples), th ...
written 7 months ago by mousheng xu10
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[edgeR Usage] Constructing DGE test with fewer input variables
... Suppose you have tumor and normal samples treated with compound A with 0, 1, 2 mM for 0, 1, 2 hours, and you want to do DGE analysis using edgeR. You want to answer the question "which genes are differentially expressed in response to compound A": after taking into account of the impact of disease c ...
edger written 7 months ago by mousheng xu10 • updated 7 months ago by Aaron Lun17k
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Comment: C: How to do multivariate glmFit analysis of RNA-seq with edgeR
... Thanks for the instructions, Aaron. ...
written 7 months ago by mousheng xu10
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Comment: C: How to do multivariate glmFit analysis of RNA-seq with edgeR
... Good catch on the -2. It's my fault -- it's actually log10(expression + 0.01) when expression = 0. 0.01 is the pseudo-count. I pasted the wrong data. However, the problems remain the same. I've made corrections to the original post. Meanwhile, dude, I really appreciate your help and sorry for the e ...
written 7 months ago by mousheng xu10

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