Question: Batch effect removal on q-RT PCR microRNA expression data
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gravatar for ivna.ivankovic
6 months ago by
ivna.ivankovic0 wrote:

I am comparing the expression of four miRNAs between 34 patients and 4 controls. The data are obtained by q-RT PCR, SYBR green method. Mean Ct values are used.

To increase the number of control samples I downloaded the dataset from EMBL-EBI Array Express database and I want to integrate 10 more controls to my dataset. In their experiment they used q-RT PCR but with Taqman method.

Any recommendations on how to correct for a batch effect would be extremely appreciated.

pcr taqman mirna R batcheffect • 214 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe47k • written 6 months ago by ivna.ivankovic0
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gravatar for Kevin Blighe
6 months ago by
Kevin Blighe47k
Kevin Blighe47k wrote:

How were you planning to process the data? - you should be able to specify a formula for the purposes of deriving p-values and other test statistics, in which case you could include batch as a covariate in such a formula.

For example:

outcome ~ gene + batch

This can then be used with t.test(), aov(), lm(), glm(), etc. This has the effect of adjusting for the effects of batch.

You may also take a look at the qpcR package in R.

Even with 34 vs 14, it is still an unbalanced dataset.

Kevin

ADD COMMENTlink written 6 months ago by Kevin Blighe47k
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