qsea makeTable()
Hello!
After using the makeTable() function in the qsea package I notice that only some of my samples have NA where the beta values should be for certain regions.
Does anyone have an explanation for why this occurs?
bioconductor
qsea
r
maketable
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
champ.norm task 1 failed - "could not find function "blc""
written by zkun8638 1When using champ.norm to process the data, the following error occurred. And it doesn‘t work and shows the same error after I load the RPMM …
-
Why does minfi impute actual values in place of NULL values when normalizing methylation data?
written by sbdejene 0Hello, I have a methylation file with raw beta values that I am trying to normalize. There are some probes excluded from the data due …
-
Probe filtering beta-values from rgSet
written by moldach 13I've see many NA's for beta-values in my rgSet object (either because some probe/CpGs were specifically set NA or because of transformation from intensities to …
-
Integrating methylation in survival analysis
written by Pin.Bioinf 35Hello, I am trying to do a survival analysis with TCGA data following this tutorial: https://www.biostars.org/p/153013/ , but I want to integrate methylation data instead …
-
Converting beta value to M value (when beta=1)
written by janhuang.cn 25There are actually two questions. 1) I am using the ComBat function in sva package to adjust for batch effect (plate). Before adjusting, the beta …
-
Filtering DMRs
written by niutster 12Hi, I get a large number of DMRs by seqlm package in comparison between two tissues after filtering by p-value <0.05 , it is near …
-
Averaging TCGA 450K Methylation Data within 500bp Windows Across all Samples
written by justinburgener 0Hi Everyone, I'm fairly new to bioinformatics and data processing, but up until now I was able to find many solutions to my problems, provided …
-
Changing values in cummeRbund CuffSet-class in R
written by irritable_phd_syndrome 13I recently completed cuffdiff on my data set and now I'm trying to work with the data using cummeRbund. I would like to be able …
-
minfi: delete NA values from RGChannelSet
written by philipp24 0Dear all, it´s probably a simple question, however I can´t find a proper solution yet. I process a 450k methlyation dataset with the minfi package. …
-
Using CSAR package with ChIP-seq data: how to fix NAs generated in mappedReads2Nhits function
written by ivoryec 7I'm using trying to use CSAR (R package, bioconductor) to analyze ChIPseq data. I've read the data in from bam files using Rsamtools and converted …