Question

HTqPCR does not copy featureData when subsetting a qPCRset

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henrik.seidel ▴ 40

@henrikseidel-11484

Last seen 7.9 years ago

When subsetting a qPCRset, the current implementation fails to transfer the featureData. Here is a fix:

diff --git a/R/qPCRset.R b/R/qPCRset.R
index d400ea5..cecef29 100644
--- a/R/qPCRset.R
+++ b/R/qPCRset.R
@@ -73,6 +73,7 @@ function(x, i, j, drop=FALSE) {
                                featureCategory=featureCategory(x)[i, j, drop=FALSE],
                                flag=flag(x)[i, j, drop=FALSE])
        phenoData(out) <- phenoData(x)[j,,drop=FALSE]
+       featureData(out) <- featureData(x)[i,,drop=FALSE]
        featureNames(out) <- featureNames(x)[i]
        out
 })

htqpcr • 1.4k views

ADD COMMENT • link updated 7.8 years ago by hdvinge • 0 • written 7.9 years ago by henrik.seidel ▴ 40

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Hi Henrik,

I wanted to include your function modification but, in the corresponding folder in my R library (mylib/HTqPCR/R), I do not find any R file corresponding to the qPCRset function. I've looked around in other folders but I don't find it...

Where do you include this code? Does it belong to another package called by HTqPCR? I'm a bit confused.

Thanks a lot!

Sarah

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux release 6.9 (Carbon)

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] BiocInstaller_1.28.0 HTqPCR_1.32.0 limma_3.34.9
[4] RColorBrewer_1.1-2 Biobase_2.38.0 BiocGenerics_0.24.0

loaded via a namespace (and not attached):
[1] gtools_3.5.0          bitops_1.0-6          affy_1.56.0
[4] stats4_3.4.3          KernSmooth_2.23-15    gplots_3.0.1
[7] zlibbioc_1.24.0       gdata_2.18.0          affyio_1.48.0
[10] preprocessCore_1.40.0 tools_3.4.3           compiler_3.4.3
[13] caTools_1.17.1        tcltk_3.4.3
>

ADD REPLY • link 6.6 years ago sbcn ▴ 80

score 0 · Answer 1 · 2017-02-14

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hdvinge • 0

@hdvinge-12367

Last seen 7.8 years ago

Hi Henrik, thanks for pointing this out. I'll add it to the next release of HTqPCR. Alternatively, if you have an account, feel free to push the correction yourself. Note that I'm aware that there are currently other issues in HTqPCR that needs fixing too. Last autumn I realized that several features in the package were broken, since they relied on some formats from other packages, which had changed. Unfortunately, I realized to late to do more than the most basic patches before the Bioconductor release. Hence, there's a number of things that needs modifying prior to the next update.

ADD COMMENT • link 7.8 years ago hdvinge • 0

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I have previously worked with HTqPCR successfully and am very grateful to the developer for providing this package. However, I am also having trouble trying to subset using HTqPCR (v1.28.0), as the sample names get lost. I am wondering if there is any idea when there might be a fix for this?

ADD REPLY • link 7.7 years ago s.corley ▴ 30