User: sharvari gujja

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20
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New User
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United States
Last seen:
4 months ago
Joined:
5 years, 1 month ago
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s*****@gmail.com

Posts by sharvari gujja

<prev • 26 results • page 1 of 3 • next >
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ComBat error: "The covariate is confounded with batch! "
... Hi, I am trying run ComBat on methylation data to correct by plate and using experimental group as cancer type. However, I get an error ``` > mMat = model.matrix(~as.factor(cancer), data=pheno) cbMat = > ComBat(dat=as.matrix(hmMat), batch=pheno$plate, mod=mMat, > par.prior=TRUE, prior.pl ...
#combat written 4 months ago by sharvari gujja20 • updated 4 months ago by James W. MacDonald50k
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Comment: C: edgeR for time series
... Thank you so much, Gordan. This is very helpful. ...
written 6 months ago by sharvari gujja20
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Comment: C: edgeR for time series
... Dear Gordan, Thank you for the reply, The data is single cell RNAseq data where condition1 is genotype1 and condition2 is genotype2 for three time points. The data is processed for edgeR analysis using the workflow mentioned in the link below: https://bioconductor.org/packages/release/bioc/vignett ...
written 6 months ago by sharvari gujja20
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Comment: C: edgeR for time series
... My question was to get your feedback about the approach I am using for this multiple time point data analysis, as I have not analyzed time series data before. Or, if you recommend using ANOVA-like test instead. Sorry about the garbled text. The conditions at different time points are: sample ...
written 6 months ago by sharvari gujja20
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edgeR for time series
... Hi, I am writing to clarify on the design matrix for running edgeR on data with multiple time points with two conditions. condition time Group sample1 condition1 T0 c1.to sample2 condition2 T0 c2.t0 sample3 condition1 T1 c1.t1 sample4 condition2 T1 c2.t1 sample5 condition1 T2 c1.t2 sam ...
edger written 6 months ago by sharvari gujja20 • updated 6 months ago by Gordon Smyth38k
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Comment: C: newSCESet and SingleCellExperiment basic differences and TMM Normalization
... Hi Aaron, I have a similar situation where I am trying to reproduce earlier results for which normalizeExpr command was used. Previous code: sce <- computeSumFactors(sce, sizes=seq(20, 80, 5)) sce <- normaliseExprs(sce, method = "TMM") Commands using edgeR TMM method: (Approach 1) norm ...
written 6 months ago by sharvari gujja20
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WGCNA chooseOneHubInEachModule Error
... Dear Peter, Steve, I am writing to seek your help in using 'chooseOneHubInEachModule' function from the WGCNA package. I am trying to generate hierarchical clustering plot on my data matrix with samples from two groups.  https://rdrr.io/cran/WGCNA/man/orderBranchesUsingHubGenes.html However, usi ...
wgcna chooseonehubineachmodule written 9 months ago by sharvari gujja20
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Comment: C: goseq with hypergeometric method
... Hello Gordon, Thank you for the reply. My concern was not getting more enriched GO terms using hypergeometric option and if I was missing any other parameter. Your explanation is helpful. Thanks ...
written 13 months ago by sharvari gujja20
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goseq with hypergeometric method
... I am running GOseq for mouse data using ~800 genes as input and ~8K genes as background lists.  Running GOseq I get the same number of enriched GO terms using Wallenius and hypergeometric methods. "9 enriched primary GO terms found at BH corrected p-value <= 0.05" Can you please suggest how th ...
goseq written 13 months ago by sharvari gujja20 • updated 13 months ago by Gordon Smyth38k
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Answer: A: Error in "getGSEDataTables" in GSEquery package
... Hello, I get the same error, and wondered if you have any suggestions to fix it. Thanks Sharvari ...
written 2.6 years ago by sharvari gujja20

Latest awards to sharvari gujja

Popular Question 11 months ago, created a question with more than 1,000 views. For RUVSeq DE analysis for data with replicate samples and 4 conditions
Popular Question 2.6 years ago, created a question with more than 1,000 views. For RUVSeq DE analysis for data with replicate samples and 4 conditions

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