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hansenlab / minfi

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getProbeType return different length of probe types #182

Open ShannonSzeto opened 5 years ago

ShannonSzeto commented 5 years ago

Hi,

I was trying to get probe type for my 850K data, but when I run: probe.type <- getProbeType(MSet, withColor = TRUE) the length of probe.type is different from the number of rows in the Meth or Unmeth matrix: Meth <- minfi::getMeth(MSet) Unmeth <- minfi::getUnmeth(MSet)

dim(Meth) [1] 866091 192 length(probe.type) [1] 865859

Any idea why this happen?

thank you very much!

kasperdanielhansen commented 5 years ago

From you description it sounds like a bug. I'll take a look.

On Fri, Mar 22, 2019 at 2:23 PM Yihsuan (Shannon) Tsai < notifications@github.com> wrote:

Hi,

I was trying to get probe type for my 850K data, but when I run: probe.type <- getProbeType(MSet, withColor = TRUE) the length of probe.type is different from the number of rows in the Meth or Unmeth matrix: Meth <- minfi::getMeth(MSet) Unmeth <- minfi::getUnmeth(MSet)

dim(Meth) [1] 866091 192 length(probe.type) [1] 865859

Any idea why this happen?

thank you very much!

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ShannonSzeto commented 5 years ago

another unrelated question, in the function getOOB, why the return "Green" take the TypeI-red address and returned "Red" take the TypeI-green address?

Thanks again!

getOOB <- function(object) {

Check input

.isRGOrStop(object)

# Extract data to pass to low-level functions that construct `Red` and `Grn`
Red <- getRed(object)
Green <- getGreen(object)
IRed <- getProbeInfo(object, type = "I-Red")
IGreen <- getProbeInfo(object, type = "I-Green")

# Extract OOB probes
list(Grn = .getOOB(Green, IRed), Red = .getOOB(Red, IGreen))

}

kasperdanielhansen commented 5 years ago

Thats what out-of-band probes are.

On Fri, Mar 22, 2019 at 2:43 PM Yihsuan (Shannon) Tsai < notifications@github.com> wrote:

another unrelated question, in the function getOOB, why the return "Green" take the TypeI-red address and returned "Red" take the TypeI-green address?

Thanks again!

getOOB <- function(object) {

Check input

.isRGOrStop(object)

Extract data to pass to low-level functions that construct Red and Grn

Red <- getRed(object) Green <- getGreen(object) IRed <- getProbeInfo(object, type = "I-Red") IGreen <- getProbeInfo(object, type = "I-Green")

Extract OOB probes

list(Grn = .getOOB(Green, IRed), Red = .getOOB(Red, IGreen))

}

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ShannonSzeto commented 5 years ago

got it. the opposite color. Thanks!

kasperdanielhansen commented 5 years ago

Ok, I cannot replicate this with standard data

library(minfiDataEPIC) length(getProbeType(MsetEPIC)) [1] 866836 dim(MsetEPIC) [1] 866836 3 length(getProbeType(MsetEPIC, withColor = TRUE)) [1] 866836

Can I get some more details wrt. what you are doing. Perhaps send me the first 2 samples of your RGChannelSet. Also check validObject(MSet)

On Fri, Mar 22, 2019 at 2:47 PM Yihsuan (Shannon) Tsai < notifications@github.com> wrote:

got it. the opposite color. Thanks!

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ShannonSzeto commented 5 years ago

Meth_file_temp_0327.RData https://drive.google.com/file/d/15jSVVis-ixVypa9fVd8mYHRMB4mQEqq9/view?usp=drive_web

On Sat, Mar 23, 2019 at 11:08 PM Kasper Daniel Hansen < notifications@github.com> wrote:

Ok, I cannot replicate this with standard data

library(minfiDataEPIC) length(getProbeType(MsetEPIC)) [1] 866836 dim(MsetEPIC) [1] 866836 3 length(getProbeType(MsetEPIC, withColor = TRUE)) [1] 866836

Can I get some more details wrt. what you are doing. Perhaps send me the first 2 samples of your RGChannelSet. Also check validObject(MSet)

On Fri, Mar 22, 2019 at 2:47 PM Yihsuan (Shannon) Tsai < notifications@github.com> wrote:

got it. the opposite color. Thanks!

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.

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ShannonSzeto commented 5 years ago

Dear Dr. Hansen, Please let me know if you have problem accessing the sample data.

Thanks!