NAN value in the Data files

[yancychy]

No description provided.

[BogdanBintu]

Dear Yang Chen,
My apologies, the percentage of nan's is 5-10%. This percentage of dim/low confidence spots that were removed form the analysis appear scholastically across the regions in each cell. Because the percentage is low we recommend ignoring the nan's in the analysis (i.e. using numpy's nanmedian function.)

[yancychy]

Ok, thanks very much.

[yancychy]

Dear BogdanBintu,
I checked the 3D structure of the A549 using sample 1902. One point is far away than other points. Is it reasonable? Or should I remove it? Thanks.

Best

[BogdanBintu]

Very likely fitting artifact. Should remove that point. I am working on a better fitting algorithm so hopefully soon this data or newer data will be updated and will not suffer from these artifacts. Bogdan

…

On Wed, Apr 24, 2019 at 10:48 AM yancychy ***@***.***> wrote: Dear BogdanBintu, I checked the 3D structure of the A549 using sample 1902. One point is far away than other points. Is it reasonable? Or should I remove it? Thanks. [image: image] <https://urldefense.proofpoint.com/v2/url?u=https-3A__user-2Dimages.githubusercontent.com_10969560_56668882-2D47525000-2D667e-2D11e9-2D8dc1-2D0e2b4c476fa5.png&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=M4c5lUU4iwg6ZJmDySa3ie9ApO1PHXgROPxlnoz7JUE&m=dcs-Gqt64j-yg97Z__zPsiQaXGNZqEcUiaWJnfjRDik&s=mFHsmQyqS4sDwlJY7iIuoOrxMal7BAvZ3qAl8IWIbuM&e=> Best — You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BogdanBintu_ChromatinImaging_issues_1-23issuecomment-2D486274034&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=M4c5lUU4iwg6ZJmDySa3ie9ApO1PHXgROPxlnoz7JUE&m=dcs-Gqt64j-yg97Z__zPsiQaXGNZqEcUiaWJnfjRDik&s=PIi7asESfA1Z9yHa5jktJEsem949bvkASaSlCq7qkTU&e=>, or mute the thread <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABK7BKWGTGHSN4QL77CHVS3PSBXKDANCNFSM4GYND2GQ&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=M4c5lUU4iwg6ZJmDySa3ie9ApO1PHXgROPxlnoz7JUE&m=dcs-Gqt64j-yg97Z__zPsiQaXGNZqEcUiaWJnfjRDik&s=ttHlvjAaxXp9y4bNO1EPF0XRMe7BxoTGU8CkdWKwlK4&e=> .

[yancychy]

Great, thanks very much!