User: xingxd16

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xingxd160
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Posts by xingxd16

<prev • 18 results • page 1 of 2 • next >
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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 24 days ago by xingxd160 • updated 24 days ago by Aaron Lun23k
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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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks ago by xingxd160 • updated 5 weeks ago by Aaron Lun23k
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Comment: C: Why the p value and logFC calculated by limma is so small
... Good advice ! I should fitler the genes that only express in little percentage of the cells first ! So , you mean that p value and logFC are too samll are reasonable with huge number of replicates ? And can I lower the logFC threshold to identify significant expression genes , such as from log2(2) ...
written 5 weeks ago by xingxd160
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Comment: C: What`s new features in DropletUtils version 1.3.10 comapred to version 1.2.2
... Thanks Aaron. I benefit a lot from your answers ! Best Regards ...
written 5 weeks ago by xingxd160
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Comment: C: Why the p value and logFC calculated by limma is so small
... Yes , you are right ! I use limma to do my single cell analysis. The cells in one condition is about 2000+ , the cells in another condition is aboult 3500+ . I just use limma to compare this two conditions follow the "lmFit" and "eBayes" steps . ...
written 5 weeks ago by xingxd160 • updated 5 weeks ago by Gordon Smyth37k

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