User: Shi, Tao

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Shi, Tao720
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Posts by Shi, Tao

<prev • 79 results • page 1 of 8 • next >
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Answer: A: Where is 'constructOligoSetFrom' or 'constructOligoSetListFrom' function?
... I found the answer: to get the lrr and baf, one can use the 'calculateRBaf' function. The vigenettes for crlmm are pretty outdated.  Hopefully the package maintainers can update them. Thanks! Tao   ...
written 4.2 years ago by Shi, Tao720
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Where is 'constructOligoSetFrom' or 'constructOligoSetListFrom' function?
... Hi list, Trying to work through the "Preprocessing and genotyping Illumina arrays for copy number analysis" vigenette, but stuck in section 4.2, as I can't find the two functions:  'constructOligoSetFrom' or 'constructOligoSetListFrom' mentioned in this section.  'crlmm' and 'VanillaICE' packages ...
vanillaice crlmm written 4.2 years ago by Shi, Tao720
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Comment: C: reading .idat files using genotype.Illumina in crlmm
... Thanks, Matt! ...
written 4.3 years ago by Shi, Tao720
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reading .idat files using genotype.Illumina in crlmm
... Hi list, When reading .idat files into R using crlmm, can I bypass the requirement of "samplesheet" as I don't have it (I only have .idat files) and I don't have access to GenomeStudio to create it? Thanks! Tao ...
crlmm idat written 4.3 years ago by Shi, Tao720 • updated 4.3 years ago by Matthew Ritchie750
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Comment: C: Results changed after DESeq2 upgrade
... Thank you very much, Michael! Tao ...
written 4.6 years ago by Shi, Tao720
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Results changed after DESeq2 upgrade
... hi list, I recently upgraded my R to 3.1.2 and DESeq2 to 1.6.3.  I re-run some of my code on a RNAseq experiment.  Comparing to the old results (done in R 3.1.0 and DESeq2 v1.4.5), all the estimates (e.g. fold changes, p values) have changed.  It seems that the most dramatic changes happened to tho ...
deseq2 written 4.6 years ago by Shi, Tao720 • updated 4.6 years ago by Michael Love25k
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Answer: A: comisc in biomart
... Hi Jim, Thanks for the quick reply!  I saw that post, but it was earlier last year and thought they might have some work-around already.  Apperantly not.  It would be nice to bring the cosmic functionality back to biomaRt, unless there are other ways to query it from R. Best, Tao   ...
written 4.7 years ago by Shi, Tao720
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comisc in biomart
... Hi list, Do you know what happened to CosmicMart in biomaRt?  It's gone. Thanks! Tao   ...
biomart written 4.7 years ago by Shi, Tao720
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Answer: A: strange log2FoldChange estimates
... Thank you, Mike, for your quick response! ?That explains. ?Do you mind in your user guide on page 21 in the R code to make this more explicit, even I know you have mentioned it right below the R chunk. Thanks, again! Tao On Thursday, August 14, 2014 2:29 PM, Michael Love wrote: hi Tao, If ...
written 5.1 years ago by Shi, Tao720
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strange log2FoldChange estimates
... hi Michael, I have a simple RNAseq experiment: a cell line treated with a compound at various doses and time. ?Here are the htseq counts for one of gene below along with the treatment conditions and sizeFactor estimated by DESeq2. > tmp ? count sizeFactor time dose 1 11396 1.0069598 8 0 ...
rnaseq dose deseq2 written 5.1 years ago by Shi, Tao720

Latest awards to Shi, Tao

Popular Question 4.2 years ago, created a question with more than 1,000 views. For reading .idat files using genotype.Illumina in crlmm
Popular Question 4.2 years ago, created a question with more than 1,000 views. For limma: NA coefficients due to missing values

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