Question

deltaCq error in package NormqPCR

1

Entering edit mode

jacorvar ▴ 40

@jacorvar-8972

Last seen 14 months ago

European Union

Hi,

I get the following error when I type deltaCq(data, "hsa-miR-875-3p-002204"):

Error in .local(qPCRBatch, ...) : 
  given housekeeping gene, hsa.miR.875.3p.002204 not found in file. Ensure entered housekeeping genes appear in the file

However, when I do "hsa-miR-875-3p-002204" %in% featureNames(data), I get TRUE.

Could you help me to solve it?

normqpcr deltaCq qrt-pcr • 1.5k views

ADD COMMENT • link 8.9 years ago • updated 8.8 years ago jacorvar ▴ 40

score 2 · Accepted Answer · 2016-02-19

2

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 days ago

United States

This is an infelicity in the NormqPCR package. Internally it calls make.names on the housekeeping gene name:

> make.names("hsa-miR-875-3p-002204")
[1] "hsa.miR.875.3p.002204"

And you will note that hsa.miR.875.3p.00204 is not the same as hsa-miR-875-3p-002204, hence the error. You could get around this by running make.names on all your featureNames first.

featureNames(data) <- make.names(featureNames(data))

ADD COMMENT • link 8.9 years ago James W. MacDonald 67k

0

Entering edit mode

It gives me an error:

featureNames(data) <- make.names(rownames(featureData(data)))
Error in `featureNames<-`(`*tmp*`, value = character(0)) : 
  'value' length (0) must equal feature number in AssayData (384)

ADD REPLY • link 8.8 years ago jacorvar ▴ 40

score 2 · Accepted Answer · 2016-02-22

Thanks for the hint. I tried it and didn't work, since it was unable to change the feature names. Then I did the following and it worked:

fData = data.frame(row.names=paste(1:length(featureNames(data)), make.names(featureNames(data)), sep="."))

featureData(data) = new("AnnotatedDataFrame", data=fData)

featureNames(data) = rownames(featureData(data))