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I'm fairly new to coding in general and was wondering if you could help me out?
I'm attempting a Motif Analysis with Signac (https://satijalab.org/signac/articles/motif_vignette.html), and when I try the FindMarkers() function in the vignette (a function I'm aware of, is part of the Seurat package), the following error pops up for me:
"Error in WhichCells.Seurat(object = object, idents = ident.1) :
Cannot find the following identities in the object: Kp1"
The following is the script I have used to run the function:
da_peaks <- FindMarkers(
object = kidney_atac,
ident.1 = 'Kp1',
ident.2 = 'Kp2',
only.pos = TRUE,
test.use = 'LR',
latent.vars = 'nCount_peaks'
)
I have also tried ident.1 = 'Kidney.Progenitor.1' (and alike to ident.2), however I still receive the same error message regarding ident.1.
Kp1 is present in the UMAP I have generated previous to this step. And is also listed in the rds file I have been using.
I have tried troubleshooting with the following code, as I found on another discussion:
"head(x = Idents(object = kidney_atac))"
However, I receive the following WarningMessage:
"Warning messages:
1: In get(name, envir = ns) : restarting interrupted promise evaluation
2: In get(name, envir = ns) : internal error -3 in R_decompress1
3: In get(name, envir = ns) : restarting interrupted promise evaluation
4: In get(name, envir = ns) : internal error -3 in R_decompress1
5: In get(name, envir = ns) : restarting interrupted promise evaluation
6: In get(name, envir = ns) : internal error -3 in R_decompress1
7: In get(name, envir = ns) : restarting interrupted promise evaluation
8: In get(name, envir = ns) : internal error -3 in R_decompress1"
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Hi there,
I'm fairly new to coding in general and was wondering if you could help me out?
I'm attempting a Motif Analysis with Signac (https://satijalab.org/signac/articles/motif_vignette.html), and when I try the FindMarkers() function in the vignette (a function I'm aware of, is part of the Seurat package), the following error pops up for me:
"Error in WhichCells.Seurat(object = object, idents = ident.1) :
Cannot find the following identities in the object: Kp1"
The following is the script I have used to run the function:
da_peaks <- FindMarkers(
object = kidney_atac,
ident.1 = 'Kp1',
ident.2 = 'Kp2',
only.pos = TRUE,
test.use = 'LR',
latent.vars = 'nCount_peaks'
)
I have also tried ident.1 = 'Kidney.Progenitor.1' (and alike to ident.2), however I still receive the same error message regarding ident.1.
Kp1 is present in the UMAP I have generated previous to this step. And is also listed in the rds file I have been using.
I have tried troubleshooting with the following code, as I found on another discussion:
"head(x = Idents(object = kidney_atac))"
However, I receive the following WarningMessage:
"Warning messages:
1: In get(name, envir = ns) : restarting interrupted promise evaluation
2: In get(name, envir = ns) : internal error -3 in R_decompress1
3: In get(name, envir = ns) : restarting interrupted promise evaluation
4: In get(name, envir = ns) : internal error -3 in R_decompress1
5: In get(name, envir = ns) : restarting interrupted promise evaluation
6: In get(name, envir = ns) : internal error -3 in R_decompress1
7: In get(name, envir = ns) : restarting interrupted promise evaluation
8: In get(name, envir = ns) : internal error -3 in R_decompress1"
I have no idea why it won't recognise kp1.
Many Thanks in advance for any help.
Ericka J.
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