Question: estimateCellCounts - Error in combine(pDataX, pDataY) in minfi
0
gravatar for Methyl
3.6 years ago by
Methyl50
United Kingdom
Methyl50 wrote:

There is a problem with the current estimateCellCounts() function which gives the following error when running:

> combinedRGset <- combine(rgSet, referenceRGset)
Error in combine(pDataX, pDataY) : data.frames contain conflicting data:
        non-conforming colname(s): Slide

 

I tried to debug it and it seems that the problem is in the read.450k function of minfi in the current version codes the Slide Column in the RGChannelSet as a list of characters, while the one present in the FlowSorted.Blood.450k object is a factor.  

I managed to get around this by using the getKereData.R script in the script folder of FlowSorted.Blood.450k where I generate a new reference dataset (I had to edit this code as well as otherwise it will give an error).  

Please take note to fix this in the next version.

 

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] FlowSorted.Blood.450k_1.8.0 minfi_1.16.0
 [3] bumphunter_1.10.0           locfit_1.5-9.1
 [5] iterators_1.0.8             foreach_1.4.3
 [7] Biostrings_2.38.0           XVector_0.10.0
 [9] SummarizedExperiment_1.0.1  GenomicRanges_1.22.1
[11] GenomeInfoDb_1.6.1          IRanges_2.4.1
[13] S4Vectors_0.8.1             lattice_0.20-33
[15] Biobase_2.30.0              BiocGenerics_0.16.1
[17] BiocInstaller_1.20.0

ADD COMMENTlink written 3.6 years ago by Methyl50
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