User: xingxd16

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xingxd160
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Posts by xingxd16

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Comment: C: Some questions for remove batch effect by using mnnCorrect
... Sincere thanks, Aaron. Best wishes. ...
written 7 weeks ago by xingxd160
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Comment: C: Some questions for remove batch effect by using mnnCorrect
... Thanks a lot Aaron !!! I still confused with somethings. - (1) Whats the difference between mnnCorrect and fastMNN? From the method name maybe the fastMNN is more faster than mnnCorrect. My data is so big , can you give me a example that to illustrate how to use BPPARAM=SerialParam() to make ...
written 7 weeks ago by xingxd160
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Some questions for remove batch effect by using mnnCorrect
... Hi all : - I use 10X single cell gene expression to perform my samples. I have 9 samples now, however when I merge them together to analysis, I can find a obviously batch effect drived by each samples. Especially, T cells are clustered by each sample rather than cell types . So I want to employ ...
batch effect scran mnncorrect single cells written 8 weeks ago by xingxd160 • updated 8 weeks ago by Aaron Lun24k
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Can DropletUtils Package be used to identify cells for 10X VDJ data ?
... Hi all : - The 10X document says the cell calling algorithm for expression data and TCR data are quite different . I want to make sure that if I can still use the DropletUtils to identify cells in 10X 5` TCR data. If can , how to perform , which functions shold I employ and which paramaters shouls ...
dropletutils 10x 5` tcr single cells written 12 weeks ago by xingxd160 • updated 12 weeks ago by Aaron Lun24k
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Comment: C: Can I ignore the warnings in limma show " Coefficients not estimable" after batc
... Good explainations and good adives !!! Sincere thanks. ...
written 3 months ago by xingxd160
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Comment: C: Can I ignore the warnings in limma show " Coefficients not estimable" after batc
... Sorry, how about now? ...
written 3 months ago by xingxd160
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Comment: C: Can I ignore the warnings in limma show " Coefficients not estimable" after batc
... Sure, sorry for that. I have edit my question. Hope you reply ! ...
written 3 months ago by xingxd160
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Comment: C: How to identify real cells in 10X RNA-seq ?
... Hi , I posted a new question about limma [here][1] . Could you help me to answer and give some adives ! Best Regards [1]: https://support.bioconductor.org/p/118976/ ...
written 3 months ago by xingxd160
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Comment: C: Why the p value and logFC calculated by limma is so small
... Hi : I posted another question about limma [here][1] , could you help me to answer ! Thanks ! [1]: https://support.bioconductor.org/p/118976/ ...
written 3 months ago by xingxd160
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Can I ignore the warnings in limma show " Coefficients not estimable" after batch correct ?
... Hi all : - When I use limma to identify differentrial expression genes , I want to correct batch effect also. - My command and data information is : ``` > table(cluster) cluster control treat 368 957 > table(Exp) Exp p3 p4 LC05 LC09 LC10 LC11 LC12 370 587 21 210 19 ...
limma warnings batchcorrect written 3 months ago by xingxd160 • updated 3 months ago by Aaron Lun24k

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