How to eliminate batch effect using removeBatchEffect function for tissue expression profiles?
For meta-analysis work, I would like to combine two rice GEO series( GSE27988 and GSE27856 ) where each series analyze multiple anatomical tissue related expression profiles.To eliminate batch effect, I'm not sure whether I can use limma removeBatchEffect function as given below. Similar posts I see related to batch effect are generally control vs treatment.
libraray(limma)
batch <- c("A","A","A",... "B","B","B") # 24 samples in batch A and 14 samples in batch B
corrected<- removeBatchEffect(data, batch)
• 2,716 views
•
link
updated
by
zx8754
•
written
by
rice.researcher
•
written
by
rice.researcher
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to analyse GSE Series with Multiple Platforms using R?
written by Prateek •
-
Where do I share a single-cell dataset?
written by Lluís R.
-
negative geo value analysis
written by linouhao •
-
Non-zero chrY CpG sites in female samples
written by lotus28
-
Error when reading microarray idat files from illumina
written by salamandra
-
Multiplatform batch correction using combat
written by Devyani •
-
NCBI GEO/GSM/SRA conventions: Is raw data a part of the SRA or a supplementary file?
written by abe •
-
Finding Gene Symbols for Probes in Raw Data
written by samet •
-
Map from GEO samples' name to TCGA name
written by landscape95
-
Job: RNA Seq. analysis tutor for specific datasets for visually impaired student needed
written by tfhahn •
i'd rather suggest BatchQC for batch effect removal + visualization + statistics https://bioconductor.org/packages/release/bioc/html/BatchQC.html