Error: if (any(which.row)) { : missing value where TRUE/FALSE needed

[pcr08]

Hej!
I am trying to run BayesPrism following the tutorial. I am using the same reference, cell state and cell type, but with my own mixture. Instead of running all the matrix, I am taking a small subset to need less time for this testing:

ref2 <- sc.dat[1:200, 1:400]
mixture2 <- m2[1:100,20500:30000]
cell_st2 <- cell.state.labels[1:200]
cell_t2 <- cell.type.labels[1:200]
myPrism2 <- new.prism(reference=ref2, mixture = mixture2, input.type = "count.matrix", cell.state.labels = cell_st2,cell.type.labels = cell_t2, key = "tumor", outlier.cut = 0.01, outlier.fraction = 0.1)
by <- run.prism(prism = myPrism2)

When I get to run this, I get this error on the run.prism function:

What could it be? How should I fix it? I already checked if any of the objects have NA values, but none has.
Thank you!

Paula

[tinyi]

Hi Paula, Thank you for your interest in our methods. Do you mind sending me the input data that can reproduce the error to ***@***.*** ? You can dump everything into a rdata file by doing save.image (file="input.rdata"). Thanks. Best, Tinyi

…

On Wed, Oct 18, 2023 at 7:26 AM pcr08 ***@***.***> wrote: Hej! I am trying to run BayesPrism following the tutorial. I am using the same reference, cell state and cell type, but with my own mixture. Instead of running all the matrix, I am taking a small subset to need less time for this testing: ref2 <- sc.dat[1:200, 1:400] mixture2 <- m2[1:100,20500:30000] cell_st2 <- cell.state.labels[1:200] cell_t2 <- cell.type.labels[1:200] myPrism2 <- new.prism(reference=ref2, mixture = mixture2, input.type = "count.matrix", cell.state.labels = cell_st2,cell.type.labels = cell_t2, key = "tumor", outlier.cut = 0.01, outlier.fraction = 0.1) by <- run.prism(prism = myPrism2) When I get to run this, I get this error on the run.prism function: [image: image] <https://user-images.githubusercontent.com/52033249/276229107-d3a42381-624d-46b8-8c9d-5d085ab2c955.png> What could it be? How should I fix it? I already checked if any of the objects have NA values, but none has. Thank you! Paula — Reply to this email directly, view it on GitHub <#60>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHS72FWSSZJ6M6ZXWKM3X764E5AVCNFSM6AAAAAA6FLE7W2VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE2DSNJRGIZDENA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[pcr08]

Hi,
I tried to attach it, let me know if you need something else or how I can solve this.
Thank you,

Paula

input2.zip

[tinyi]

Hi Paula, You only have one cell type. This will cause errors. The number of cell types should also be greater than 1, otherwise there is no need for deconvolution. Please refer to the vignette for the definition of cell types. Best, Tinyi

…

On Wed, Oct 18, 2023 at 4:52 PM pcr08 ***@***.***> wrote: Hi, I tried to attach it, let me know if you need something else or how I can solve this. Thank you, Paula input2.zip <https://github.com/Danko-Lab/BayesPrism/files/13033854/input2.zip> — Reply to this email directly, view it on GitHub <#60 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHS3B4KP57ZI43PU5SJ3YAA6MDAVCNFSM6AAAAAA6FLE7W2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONRZGMYDCMBVGM> . You are receiving this because you commented.Message ID: ***@***.***>

[pcr08]

Hi,
it is true, now I realised, sorry!
Thank you so much!