User: shao

gravatar for shao
shao80
Reputation:
80
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Location:
Germany
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4 months, 1 week ago
Joined:
4 years, 7 months ago
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c*****@dkfz.de

Posts by shao

<prev • 19 results • page 1 of 2 • next >
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single-cells RNA-seq analysis by MAST with unbalanced group size
... We have single-cells sequencing data from two groups of cells with 100 cells and 3000 cells, respectively. Our interest is to find the gene differentially expressed between these two groups, and we like to try MAST. We are worrying abou the unbalanced group size, i.e, 100 vs 3000, will it affect th ...
rna-seq single-cell mast differential analysis written 5 months ago by shao80 • updated 5 months ago by Andrew_McDavid120
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Comment: C: nthreads option does NOT work in rsubread featureCounts
... Thanks for the quick reply! I saw more than 100% CPU usage in the later stage of featureCounts (macosx binary version), the second reason explained the time usage. Would be great to have faster read for bam files. ...
written 9 months ago by shao80
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nthreads option does NOT work in rsubread featureCounts
... I increased  nthethreads value in featureCounts but the running time didnt decrease. I used the following command: subread_res <- featureCounts(files, annot.ext = GTF_file, isGTFAnnotationFile = TRUE, nthreads = X, countMultiMappingReads ...
rsubread written 9 months ago by shao80 • updated 9 months ago by Gordon Smyth33k
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Comment: C: MAST reported warning "Coefficients ... are never estimible and will be dropped.
... Thanks! Based your answer I examined the cross tables between predictors. I think Sex "U" are dropped not only because the correlation between "U" and "Refed". The Sex "U" are the samples when bathches is "b5", which are 31 in "Fast" and 55 "Refed"so one of them is redundant and dropped. I check the ...
written 14 months ago by shao80
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MAST reported warning "Coefficients ... are never estimible and will be dropped."
... Hi, I run into such warnings with MAST when fitting the hurdle model to a sc-rnaseq data. Data has been log2-transformed(log2(cpm + 1)). The model is: zlm.SingleCellAssay(~ FvF + batches + sex, sca) After fitting, MAST reported "In .nextMethod(object = object, value = value) :   Coefficients ba ...
mast sc-rnaseq written 14 months ago by shao80
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Comment: C: confusing on the interaction and betaprior in DESeq2.
... Thank a lot for your help! As DESeq2  has versatile settings for the linear regression analysis, it will be really help if you could provide more examples in vignette. ...
written 3.0 years ago by shao80
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Comment: C: confusing on the interaction and betaprior in DESeq2.
... Thanks Mike. I mean the main effect for condition (for all sets). In betaPrior = TRUE, it is achieved by results(dds, contrast=c("condition","B","A")). How do I get it in the betaPrior = FALSE setting? ...
written 3.0 years ago by shao80
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Comment: C: confusing on the interaction and betaprior in DESeq2.
... Hi Mike, Thanks a lot for your quick reply. I missed that post. In question C, I want to compare the the difference between conditions A and B ignoring set effect with "design(dds) <- ~ set + condition + set:condition" and "betaPrior = FALSE". In this case, does "condition_B_vs_A" meas the diffe ...
written 3.0 years ago by shao80
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confusing on the interaction and betaprior in DESeq2.
... Hi, I still have a few questions regarding the contrast and interaction in DESeq2 after going through the forum. 1. Test on condition effect: the difference between using group variable and interactions. There seems two ways to get the condition effect for one set basing on  the examples parts of ...
deseq2 interactions contrast written 3.0 years ago by shao80
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Comment: C: DEseq2 time-series design.
... I use the same design as you posted. ...
written 3.0 years ago by shao80

Latest awards to shao

Great Question 13 months ago, created a question with more than 5,000 views. For DEseq2 time-series design.
Popular Question 13 months ago, created a question with more than 1,000 views. For multiple level factors contrast in nbinomLRT, DESeq2.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For multiple level factors contrast in nbinomLRT, DESeq2.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DEseq2 time-series design.

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