User: Ying W

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Ying W90
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Posts by Ying W

<prev • 12 results • page 1 of 2 • next >
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Answer: A: TMM Manual Calculation to be used in MATLAB on miRNA count data
... It might be easier to port the MATLAB calculations to R instead of porting the R libraries to MATLAB. I've looked into the TMM normalization before and unless you have a good feel for R + C, you can have a look at the source code for edgeR here: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/R ...
written 4.5 years ago by Ying W90
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Comment: C: Problem in analysing microarray data with ComBat
... it looks like you are having a mismatch between number of rows that combat is reading in with the number of data rows that you have, you probably also want to check why the value is NA ...
written 4.5 years ago by Ying W90
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Answer: A: DiifBind version difference
... There were several changes to heatmap since 1.8.5 http://www.bioconductor.org/packages/release/bioc/news/DiffBind/NEWS Easiest solution would probably be to downgrade until task is done unless you want to dig through code. Did you forget to attach error/code for heatmap side colors? ...
written 4.5 years ago by Ying W90
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Comment: C: Problem in analysing microarray data with ComBat
... Please show the top couple lines of your csv file to help in troubleshooting, also what version of ComBat are you running (the function in SVA library?). You need to specify a batch categorical variable that corresponds to the effect you are trying to remove.   ...
written 4.5 years ago by Ying W90
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Comment: C: DEseq for chip-seq data normalisation
... Hi Rory, From my understanding, TMM normalization will try to minimize the fold changes between conditions (assumes that most regions are not differentially expressed) and works best with about equal number of up and down regulated genes (For the second part see some of the work done by Kadota K. o ...
written 6.1 years ago by Ying W90
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Answer: A: DEseq for chip-seq data normalisation
... Hi Rory, Could you give some insight into why TMM is used with full library size, it seems to make sense for effective library size case but where full library size is used, would it still be valid to try and minimize changes between conditions? Best, -Ying On 11/05/13 18:18, Rory Stark wrote: &g ...
written 6.1 years ago by Ying W90
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Large logCPM values when using offsets in edgeR for normalization
... Dear list, I am interested in adjusting for GC bias in my experiment. I have my data in an "SeqExpressionSet" object (using EDASeq library) called eset and I then run the following commands: dataOffset = withinLaneNormalization(eset,"gc", which="full",offset=TRUE) dataOffset2 = betweenLaneNormaliza ...
sequencing edger cqn edaseq written 6.7 years ago by Ying W90 • updated 6.7 years ago by Gordon Smyth39k
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Answer: A: how to annotate Illumina HumanHT-12 v3 chips?
... The answer depends on what you are interested in biologically. If you are only interested in well-annotated coding genes for downstream pathway analysis, then only use the NM_ genes. Is there a reason why you want to combine the probes for each gene? Some software that I've used has used median/mea ...
written 6.8 years ago by Ying W90
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Chippeakanno venn
... Hi, I recently made venn diagrams from chip-seq data using the Chippeakanno library and I was wondering how to get the intersect of these venn diagrams and annotate them (closest gene, within intron/exon, distance from TSS) Thanks, Ying Wu m1 = read.table("./methyl1_peaks.bed", sep="\t") m2 = rea ...
go bsgenome annotate written 8.4 years ago by Ying W90 • updated 8.4 years ago by Julie Zhu4.1k
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Answer: A: Problem with texi2dvi
... Have you tried installing MilkTeX for windows? -- Ying Wu PhD Student Genetics, Molecular and Cellular Biology University of Southern California ...
written 8.8 years ago by Ying W90

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