estimateCellCounts with EPIC array

[YinanZheng]

Hello,

I seems current estimateCellCounts function does not support EPIC array. Is it possible that future version will add this feature or the algorithm itself may not work for EPIC array at all (e.g. missing signature CpGs in EPIC)?

Than you.

[Jfortin1]

Hi Yinan,

We are actually currently working on that and should release something in the next couple of days hopefully.

JP

[YinanZheng]

Glad to hear that. Thank you for your great work!

[Jfortin1]

We have now fixed the issue. The function estimateCellCounts() now takes EPIC array as input. We describe the changes in our bioRxiv preprint: http://biorxiv.org/content/early/2016/07/23/065490

[MeganBreitbach]

I am still getting an error when trying to estimate cell counts with EPIC data.

cellCounts_epic <- estimateCellCounts(RGset_epic) Loading required package: FlowSorted.Blood.EPIC Error in estimateCellCounts(RGset_epic) : Could not find reference data package for compositeCellType 'Blood' and platform 'EPIC' (inferred package name is 'FlowSorted.Blood.EPIC') In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘FlowSorted.Blood.EPIC’

I have tried to load the ‘FlowSorted.Blood.EPIC’ package, but also get this error-

biocLite('FlowSorted.Blood.EPIC') BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21). Installing package(s) ‘FlowSorted.Blood.EPIC’ Warning message: package ‘FlowSorted.Blood.EPIC’ is not available (for R version 3.3.1)

Additionally, I have read the bioRxiv reprint and repo in which you describe a new combineArrayTypes() function. However, there is no such function that I can find in the minfi package. Has it been included in the package yet?

[kasperdanielhansen]

Are you using Bioconductor stable or Bioconductor devel? All of Bioconductor is released every 6 months and we have no control over that. You need to use the devel version to get the new stuff.

Also, we should really better document how to do this; you first need to convert the EPIC array to 450k and then send it through estimateCellCounts.

This might help: https://github.com/hansenlab/EPIC450k_repro/blob/master/analysis/cell.R

Best, Kasper

On Fri, Sep 9, 2016 at 12:09 PM, Megan notifications@github.com wrote:

I am still getting an error when trying to estimate cell counts with EPIC data.

cellCounts_epic <- estimateCellCounts(RGset_epic) Loading required package: FlowSorted.Blood.EPIC Error in estimateCellCounts(RGset_epic) : Could not find reference data package for compositeCellType 'Blood' and platform 'EPIC' (inferred package name is 'FlowSorted.Blood.EPIC') In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘FlowSorted.Blood.EPIC’

I have tried to load the ‘FlowSorted.Blood.EPIC’ package, but also get this error-

biocLite('FlowSorted.Blood.EPIC') BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21). Installing package(s) ‘FlowSorted.Blood.EPIC’ Warning message: package ‘FlowSorted.Blood.EPIC’ is not available (for R version 3.3.1)

Additionally, I have read the bioRxiv reprint and repo in which you describe a new combineArrayTypes() function. However, there is no such function that I can find in the minfi package. Has it been included in the package yet?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kasperdanielhansen/minfi/issues/70#issuecomment-245959965, or mute the thread https://github.com/notifications/unsubscribe-auth/AEuhn719w6tQqQ_o2PV5VgVU5TR52Id-ks5qoYTPgaJpZM4JLwig .

[MeganBreitbach]

I have tried everything you have suggested and am still unable to use the combineArrays and convertArray functions.

I searched for both the combineArrays and convertArray functions in the help function of R and received this message - Error in fetch(key) : lazy-load database '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/minfi/help/minfi.rdb' is corrupt

[kasperdanielhansen]

Well, that error suggests you have some installation issues. I would reinstall the package.

But tell me the output of sessionInfo() after you have loaded minfi and also source("http://www.bioconductor.org/biocLite.R") biocValid()

Kasper

On Fri, Sep 9, 2016 at 1:21 PM, Megan notifications@github.com wrote:

I have tried everything you have suggested and am still unable to use the combineArrays and convertArray functions.

I searched for both the combineArrays and convertArray functions in the help function of R and received this message - Error in fetch(key) : lazy-load database '/Library/Frameworks/R. framework/Versions/3.3/Resources/library/minfi/help/minfi.rdb' is corrupt

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kasperdanielhansen/minfi/issues/70#issuecomment-245979953, or mute the thread https://github.com/notifications/unsubscribe-auth/AEuhn0IRk-bjUgBqdXGVJ2o2W79UjjpBks5qoZWSgaJpZM4JLwig .

[MeganBreitbach]

That worked. Here is the output-

source("http://www.bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.23.9), ?biocLite for help biocValid() [1] TRUE sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] BiocInstaller_1.23.9

loaded via a namespace (and not attached): [1] tools_3.3.1

Thanks so much!

[kasperdanielhansen]

solved; closing.