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HenrikBengtsson / illuminaio

🔬 R package: This is the Bioconductor devel version of the illuminaio package.
http://bioconductor.org/packages/devel/bioc/html/illuminaio.html
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Questions about illuminaio use #26

Open AliceCheng7 opened 10 months ago

AliceCheng7 commented 10 months ago

May I confirm whether this package can be used for get the values of illumina methylation arrays? If yes, how does it handle the value from the beads and give one value for the loci? Best, Xianying

kasperdanielhansen commented 10 months ago

As far as I know - and this is based on very old information - to get the values of the individual beads before they are aggregated into loci, you need to modify the scanner settings BEFORE the arrays are scanned by the machine. Then, the individual beads will be output in form of a text file. We currently have no support for reading in these text files, but then again, most people don't have them because of the scanning issue.

Best, Kasper

On Fri, Dec 1, 2023 at 4:53 AM AliceCheng7 @.***> wrote:

May I confirm whether this package can be used for get the values of illumina methylation arrays? If yes, how does it handle the value from the beads and give one value for the loci? Best, Xianying

— Reply to this email directly, view it on GitHub https://github.com/HenrikBengtsson/illuminaio/issues/26, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DH6XJVID5ZFVGWHB3S3YHGSIDAVCNFSM6AAAAABACSE7J2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZDANJRGM4TOMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Best, Kasper

AliceCheng7 commented 10 months ago

Hi Kasper, Thank you so much for your quick reply. Yes, We scanned the beadchip in a right way. Do you know whether it can read illumina epic v2 data? Do you have any experience on it? We can get most markers have the similar beta values using illuminaio (idat files) comparing Genomestudio. But we found some loci's ( a very small number)Signal of methylated and unmethylated are quite different from GenomeStudio. So we want to know why the intensity of A and B have difference? Best, Xianying

kasperdanielhansen commented 10 months ago

That is very weird. Could you send me the two IDATs for a sample, the Genome Studio output and an identifier for which probes you're talking about?

We have looked at this in the past for earlier arrays, but not for the Epic v2, but I don't see why anything should have changed.

Best Kasper

On Fri, Dec 1, 2023 at 10:23 AM AliceCheng7 @.***> wrote:

Hi Kasper, Thank you so much for your quick reply. Yes, We scanned the beadchip in a right way. Do you know whether it can reads illumina epic v2 data? We can get most markers have the similar beta values using illuminaio comparing Genomestudio. But we found some loci's ( a very small number)Signal of methylated and unmethylated are quite different from GenomeStudio. So we want to know why the intensity of A and B have difference? Best, Xianying

— Reply to this email directly, view it on GitHub https://github.com/HenrikBengtsson/illuminaio/issues/26#issuecomment-1836300384, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DH5RYE2C6JCS2KLD36TYHHZAPAVCNFSM6AAAAABACSE7J2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZWGMYDAMZYGQ . You are receiving this because you commented.Message ID: @.***>

-- Best, Kasper

AliceCheng7 commented 10 months ago

Hi Kasper, Could you use the demo data from illumina support site: 206891110001.zip Here is the product info: https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html We found the inconsistent loci mostly have a BO or TO design. see the info about TO and BO design. image Here is the list: target.txt Thank you so much for your help. Best, Xianying

AliceCheng7 commented 10 months ago

By the way, we also found these locis seems have a high detected p value when using genomestudio. I am not sure whether if these markers have a bad bioinformatic performance (e.g. high signal deviation).

AliceCheng7 commented 10 months ago

@kasperdanielhansen Hi Kasper， May I ask do you have any update on this issue? Best, Xianying

kasperdanielhansen commented 10 months ago

You never sent the output from GenomeStudio, right? How can we make a comparison without that output?

Best, Kasper

On Mon, Dec 11, 2023 at 2:51 AM AliceCheng7 @.***> wrote:

@kasperdanielhansen https://github.com/kasperdanielhansen Hi Kasper， May I ask do you have any update on this issue? Best, Xianying

— Reply to this email directly, view it on GitHub https://github.com/HenrikBengtsson/illuminaio/issues/26#issuecomment-1849493886, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DHZQ7UJOGEU4LLHFWWLYI23PRAVCNFSM6AAAAABACSE7J2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBZGQ4TGOBYGY . You are receiving this because you were mentioned.Message ID: @.***>

-- Best, Kasper