User: Tom

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Tom10
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Posts by Tom

<prev • 31 results • page 1 of 4 • next >
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Comment: C: MethylSet to MethyLumiSet
... > library(watermelon) > x=as.methylumi(GRset.norm) also ended with the same error. Error in .validate_assayDataElementReplace(obj, value) : object and replacement value have different dimensions Any suggestion would be very welcome. ...
written 10 months ago by Tom10
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MethylSet to MethyLumiSet
... Hi all, I have several 450k and 850k (EPIC) array IDAT files. After combining them using minfi::combineArrays() and normalizing, I want to convert the object into MethyLumiSet class for downstream analysis. Because no functions are implemented for that purpose, I tried to create a new MethyLumiSet ...
methylumi minfi watermelon written 10 months ago by Tom10
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'type = genes' for RnBeads::meth() function
... Hi all, meth() function in RnBeads package accepts an option 'type' which can be set to "sites", "genes", etc. When 'type' is set to "genes", how does it compute a single beta-value representing the methylation on single gene (e.g., calculating average beta-values of the probes on promoter regions ...
rnbeads written 10 months ago by Tom10
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Comment: C: Extracting normalized DESeq2 counts for a multi-factor design?
... Thanks, I was assuming rlog/vst normalize batch-based trend when blind=FALSE. If the data has obvious batch effect and I want to do downstream analyses such as unsupervised clustering with batch effect-free expression values, would removeBatchEffect() output be more appropriate than rlogMat? ...
written 15 months ago by Tom10
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Comment: C: Extracting normalized DESeq2 counts for a multi-factor design?
... Thank you for your reply. When I do removeBatchEffect(), should the 'batch' function be set, i.e. removeBatchEffect(rlogMat, batch=MyBatch)? With 'batch=NULL', I only got the same matrix as the input rlogMat, and with 'batch=MyBatch', the output matrix was somewhat different. Because, as far as I ...
written 15 months ago by Tom10
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Comment: C: Extracting normalized DESeq2 counts for a multi-factor design?
... Michael, How can I modify the model and extract batch effect-normalized counts in R commands? Or do I have to overwrite some implemented functions? Tom ...
written 15 months ago by Tom10
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Answer: A: DESeq2 rlog as input for GAGE
... Luo and Michael, Thank you for your helpful comments. I will use rlog transformed data as an input for downstream GAGE analysis. Best, Tom ...
written 17 months ago by Tom10
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Comment: C: UCSC web service API
... You don't need to uninstall the old version of rtracklayer. Just set dev_mode(on=T) and load rtracklayer every time you need the development version. ...
written 17 months ago by Tom10
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DESeq2 rlog as input for GAGE
... Dear all, In the vignette of GAGE pathway analysis package, a joint workflow with DESeq2 is shown, where only the column of log2 fold change from DESeq2 output is used as an input for GAGE. Is rlog matrix calculated by DESeq2 applicable as an input for GAGE pathway analysis? Any comments would be ...
gage deseq2 written 17 months ago by Tom10
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Answer: A: CopywriteR error: "Error in .Method"
... I looked inside the Copywriter.log file and it ended with: INFO [2016-07-12 14:35:29] remote-error in value[[3L]](cond): failed to open BamFile: file(s) do not exist:   ‘XXX(one of my bam files).bam’ I corrected the wrong path and then CopywriteR() ended successfully.   ...
written 17 months ago by Tom10

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