estimateCellCounts - Error in combine(pDataX, pDataY) in minfi
0
0
Entering edit mode
Methyl ▴ 50
@methyl-8470
Last seen 5.9 years ago
United Kingdom

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

minfi FlowSorted.Blood.450k • 762 views
ADD COMMENT

Login before adding your answer.

Traffic: 145 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6