User: sinha.puja

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sinha.puja0
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Posts by sinha.puja

<prev • 12 results • page 1 of 2 • next >
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Error while running ChAMP pipeline
... When running ChAMP pipeline, the step SVD.plot initially gives no batch effect but after running 5-6 times with the same data it is giving batch effect. Is this possible..???? Another problem is that at step myDMP, in the argument adjPVal, changing the cutoff and running the pipeline with the same ...
champ.dmr written 3 months ago by sinha.puja0
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Comment: C: error while using champ.svd() function
... Hi Yuan, I tried using as.character function but again it gives me the same type of error as mentioned in the upper section. ...
written 4 months ago by sinha.puja0
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Comment: C: Error while using champ.svd() function in subset of data
... Hi, I am also facing the same problem as you mentioned above. Your colleague wrote something about solution but I didn't get your arguments. Can you be able to explain me your function to resolve this..? Thanks! ...
written 4 months ago by sinha.puja0
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Comment: C: error while using champ.svd() function
... My code is: if (!requireNamespace("BiocManager", quietly=TRUE))   install.packages("BiocManager") BiocManager::install("ChAMP") library(ChAMP) baseDir2 <- "/C:/Users/sinha.puja/Desktop/idats" myLoad <- champ.load(directory = getwd(),arraytype="EPIC") champ.QC() myNorm <- champ.norm(beta=my ...
written 4 months ago by sinha.puja0
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error while using champ.svd() function
... Hi, I am trying to analyze Illumina EPIC methylation array data with Champ. and getting the following error when run champ.svd() : << PhenoTypes.lv generated successfully. >> Error in summary(lm(svd.o$v[, c] ~ PhenoTypes.lv[[f]]))$coeff[2, 4] : subscript out of bounds Any ideas o ...
champ written 4 months ago by sinha.puja0
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Comment: C: ChAMP Methylation analysis error code "could not find function champ.load"
... I tried to use tab key in R and it shows no matches. Also while installing ChAMP I got the following warning messages: ERROR: failed to lock directory 'C:/Users/sinha.puja/Documents/R/win-library/3.5' for modifying Try removing 'C:/Users/sinha.puja/Documents/R/win-library/3.5/00LOCK-IlluminaHumanMe ...
written 4 months ago by sinha.puja0
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ChAMP Methylation analysis error code "could not find function champ.load"
... Hi..I tried to use ChAMP for my EPIC methylation array data and I use the following commands but it's not working, if (!requireNamespace("BiocManager", quietly = TRUE))   install.packages("BiocManager") BiocManager::install("ChAMP", version = "3.8") a BiocManager::install("ChAMPdata", version = "3. ...
champ written 4 months ago by sinha.puja0
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error during loading of minfi package
... Hi..I tried to load minfi package in Rstudio, but the loading says error:  Error: package or namespace load failed for ‘minfi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):  there is no package called ‘readr’ And when I tried to run the command, it gives me fo ...
software error written 4 months ago by sinha.puja0
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Comment: C: minfi R package for methylation analysis of infinium 450K microarray data
... I found the error and corrected it, now its working. Thanks a lot. ...
written 4 months ago by sinha.puja0
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Comment: C: minfi R package for methylation analysis of infinium 450K microarray data
... After removing the extra slash also I am getting the same type of error i.e, Error in read.metharray.sheet(baseDir) : 'base' does not exists. I am stuck at the very first step, don't know how to get rid off. If anyone else is having the same issue or know how to resolve then please respond. Thank ...
written 4 months ago by sinha.puja0

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