Does anyone succeded clustering TCGA data?
I am strugelling with TCGA to get an accurate clustering. I have tried to include many covariates and batch factors to my model using voom and removeBatchEffect(). The problem is my PCA is not satisfactory for me as there is always some points that cluster aways from similar condition and different conditions that overlaps.
Most of the studies I have read so far have not reported the clustering results. They said they accounted for the batch.
So, what is your experiences? Does any one succesfully removed the batch effect and clustered the data?
• 755 views
•
link
updated
by
Biostar
•
written
by
Omar Mohamed •
•
written
by
Omar Mohamed •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
CombatSeq introduces clustering in RNA-seq data (miRNA)
written by ben.j.wendel •
-
Adjusting for covariates such as duration of diabetes, age, sex and BMI
written by sukeshinik5 •
-
Removing batch effect and doing differential gene expression analysis
written by sarahlee.bekaert •
-
Two rounds of batch effect removal
written by Kazuna •
-
Should I cluster and PCA the whole sample or only the genes of interest?
written by Omar Mohamed •
-
How to curate ChIP-seq data, then normalize the depth?
written by Omar Mohamed •
-
PCA plot after batch normalization
written by parinv •
-
Batch effect problem DEG, DESseq2
written by maria2019
-
Pre-processing of RNA-Seq data for WGCNA
written by gokce.ouz
-
Evaluating removing batch effect tools with PCA or MDS?
written by Lluís R.
