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Description:
This is a forum for the users of the ComBat software for adjusting for batch effects.
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Do I need to normalize data if I use ComBat?
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Dear all, I'm practically biologist and nearly know nothing about meta-analysis of gene expressions. I plan to use ComBat with affymatrix expression data (CEL files) acquired from three different experiments. Do I need to normalize data if I use ComBat? If so, I should normalize the data before or after reducing batch effect by ComBat?... more »
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normalization across different mRNA arrays and reagents
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To whom it may concern,
I am facing a really complex situation and I would really
appreciate it if you could help me or give me any suggestions:
Let’s call experiment 1 = my patients RNA samples (n=19, RNA
extracted from peripheral blood mononuclear cells-PBMCs) have already been... more »
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Error in solve.default(t(design) %*% design)
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Hi,
I am trying to use ComBat and I should say it is a much needed tool
given the various platform the data comes through. I have a gene
expression data that was obtained using two batches. I downloaded
ComBat and used it as it was specified in the Usage documentation and
I run into this error,... more »
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DABG filtering in Combat
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Dear All,
I'm using ComBat to adjust for batch effect on Human Exon arrays datasets.
I've never used it on any other kind of data.
My question is related to the DABG filtering:
I have two distinct objects (numerical matrices): the expression matrix and
the DABG matrix (containing the p-values for the detection call for each... more »
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Use of Combat
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Hello,
I would like to use the combat method to adjust batch effects in
microarray data, but was wondering your opinion on the use of combat
on:
a) a full set of genes or using a subset ( most variable genes across
arrays)
b) whether the data must be standardized expression (as described in... more »
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removing batch effect at exon level
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Hi,
i have used the combat to remove the batch effect at the gene level
from the gene expression data sheet , and it worked very nicely.
i was wondering if i can do the same thing at the exon level using the
exon spread sheet ?
i m using affymetrix mouse exon arrays
please let me know , i need to remove the batch effect from my data at... more »
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