Prep function not working with multiple IDAT/sdfs

[biostars-nyc]

I ran the following two commands, according to the vignette, which should produce vastly different results. I've also noticed that the "func = NULL" does NOT return a Sig object, but instead a matrix of beta values (as with func = getBetas). How do I process several IDAT files at once? The lapply solution doesn't work because this produces a list of Sig objects, which I then can't merge in any reasonable way for pre-processing and normalization...

sdfs = openSesame(idat_dir, func = NULL)

sdfs = openSesame(idat_dir, prep = 'QHDPB', func = NULL

[zwdzwd]

I tried the following example with a dir input, it does seem to return a list of SigDFs. does this work for you?

a = openSesame(system.file("extdata", "", package = "sesameData"), func=NULL)
str(a)

do you mean something like

do.call(c, lapply(prefixes, openSesame, ...))

?

technically you don't need it since you can just use openSesame(prefixes), if you really want to do it in steps, you can still

sdfs = openSesame(prefixes, func=NULL, prep="Q")

then

sdfs = openSesame(sdfs, func=NULL, prep="S")

[biostars-nyc]

Unfortunately those steps don't work for me, because the first function results in a matrix with beta values (even with func = NULL). The prefixes object is my IDAT directory, with two files for each sample. Thus, when I perform the second function, a NULL sdfs object is returned:

sesameDataCache()

snapshotDate(): 2022-07-22

[1] TRUE

idat_dir = getwd()

sdfs = openSesame(idat_dir, func = NULL, prep = 'Q')

class(sdfs)

[1] "matrix" "array"

sdfs = openSesame(sdfs, func=NULL, prep="S")

sdfs

NULL

On Tue, Aug 9, 2022 at 3:51 PM Wanding Zhou - Bioinformatics < @.***> wrote:

I tried the following example with a dir input, it does seem to return a list of SigDFs. does this work for you?

a = openSesame(system.file("extdata", "", package = "sesameData"), func=NULL) str(a)

do you mean something like

do.call(c, lapply(prefixes, openSesame, ...))

technically you don't need it since you can just use openSesame(prefixes), if you really want to do it in steps, you can still

sdfs = openSesame(prefixes, func=NULL, prep="Q")

then

sdfs = openSesame(sdfs, func=NULL, prep="S")

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[zwdzwd]

I wonder if that could be a version difference.

On my end

idat_dir = openSesame(system.file("extdata", "", package = "sesameData"), func=NULL) sdfs = openSesame(idat_dir, func = NULL, prep = 'Q') class(sdfs) [1] "list"

What is your package versions?

sapply(c("sesame","sesameData","ExperimentHub"),

• function(x) as.character(packageVersion(x))) sesame sesameData ExperimentHub "1.15.6" "1.14.0" "2.4.0"

[biostars-nyc]

Is sdfs not a list after the first function for you?

R/4.1.1

sesame 1.12.9

sesameData 1.12.0

ExperimentHub 2.2.1

On Tue, Aug 9, 2022 at 4:51 PM Wanding Zhou - Bioinformatics < @.***> wrote:

I wonder if that could be a version difference.

On my end

idat_dir = openSesame(system.file("extdata", "", package = "sesameData"), func=NULL) sdfs = openSesame(idat_dir, func = NULL, prep = 'Q') class(sdfs) [1] "list"

What is your package versions?

sapply(c("sesame","sesameData","ExperimentHub"),

-

function(x) as.character(packageVersion(x))) sesame sesameData ExperimentHub

"1.15.6" "1.14.0" "2.4.0"

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[stefdecondor31]

Hi, I have the same problem, have you found a solution?

Stef

[zwdzwd]

I think this is most likely a version difference. Sesame switched from SigSet to SigDF to allow for more transparent storage. Updating your software version should solve this.

[stefdecondor31]

Thank for the answer

Ubuntu 22.04 R/4.1.2 sesame sesameData ExperimentHub "1.12.9" "1.12.0" "2.2.1"

[stefdecondor31]

Hi, I am trying to read my .idat files into sesame using the readIDATpair function but the soft does NOT return a Sig object, but instead a matrix. I have performed the updates. sesame sesameData ExperimentHub "1.17.8" "1.16.0" "2.6.0" R = "4.2.2"

Thanks

Stef L

[stefdecondor31]

I also have the same problem with the data from the tutorial series. Stef L

[zwdzwd]

Hi the data frame/matrix you got from readIDATpair contains raw signal intensities. If you are using an earlier version it's the SigSet, but the newer version returns SigDF which is essentially a data frame.