ComBat-seq

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Using ComBat-Seq over RSEM estimated counts

1

Hi, I have 2 RNA-Seq studies on RSEM counts only. Would it a problem using the float RSEM counts as an input to ComBat-Seq? or Should I round them? Thanks...

ali-kishk

How to adjust by multiple variables using ComBat-Seq?

3

Dear @zhangyuqing , I am trying to adjust my RNA data using ComBat-Seq since I realised that there are 3 batches that I need to adjust for: - Place (2...

evaesquinas

Hi @zhangyuqing , I am trying to run batch correction with Combat-seq package but keep running into an error. The data set has 14 variables (the first 10 belong to...

dea-jenaer

When a batch has only one level of a covariate (i.e. group) variable, the common dispersion is used for ALL GENES. Why? Shouldn't the code default to the tagwise dispersion...

reidbm

ComBat-Seq correction creating very large count values--cannot feed into DESeq2

10

Hey, Thanks for making this software, it seems really helpful (and I'd love to use it if I can get this to work). The matrix generated by ComBat-Seq cannot be...

cdharshika

ComBat_seq took a very long time

11

Hi, I was using ComBat_seq for RNA seq data, and I have covar_mod as the argument, which has 8 variables, however, it has been run more than 10 hours, and...

rongwong1119

Keep getting the error that rows do not match

1

I have a matrix with 2300 samples, and about 34 batches. I am trying to use `ComBat_Seq` on this matrix. The matrix is arranged by genes in the rows, and...

sameet-sema4

Implementation with DESeq2 > "invalid class “DESeqDataSet” object: the count data is not in integer mode"

5

Dear Yuqing, Im working on a RNA-seq meta-analysis and trying to use ComBat-seq to normalize read counts previous to DESeq2 analysis. Im using the following command to normalize the counts...

samuellup

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

9

Hi, I am using ComBat-seq to remove batch effects from my dataset, and then running DESeq2 on the same. I was wondering if I could use the same data, after...

sharvarinarendra

hi,I am confused to use the combat_seq to deal with my RNAseq data .I have two batchs and I have thress groups such as groupA vs groupB,groupA vs groupC.How I...

yirenheihei