Errors in using getMarkerFeatures

[sa95078]

When using getMarkerFeatures, I am getting the following error message:
Error in cor(estbgdP, obsbgdP) : incompatible dimensions
In addition: Warning messages:
1: In rbind(estbgd, obsbgd) :
number of columns of result is not a multiple of vector length (arg 1)
2: In rbind(estbgdP, obsbgdP) :
number of columns of result is not a multiple of vector length (arg 1)

this the end of the log file:
2020-07-06 20:34:21 : MatrixClass = Sparse.Double.Matrix
2020-07-06 20:34:21 : Matching Known Biases, 0.003 mins elapsed.

This happened after I renamed cell cluster identity and use the new cluster ID. When I used the original cluster ID (groupBy = "Clusters" it worked fine.

Thank you,

James

[sa95078]

I solved the problem by changing the cluster ID to characters from factors. Thanks,

[brianpenghe]

I solved the problem by changing the cluster ID to characters from factors. Thanks,

I have the same problem though my cluster ID is already in characters class. Any ideas???

[brianpenghe]

Interestingly the errors were gone when using Jupyter Notebook. That's strange.

[qdong2023]

@brianpenghe Have you saved this problem? I still encountered the same issue. Any suggestions?

markersPeaks <- getMarkerFeatures(

• ArchRProj = projmulti_match, 
  

• useMatrix = "PeakMatrix", 
  

• groupBy = "cell_annotation",
  

• bias = c("TSSEnrichment", "log10(nFrags)"),
  

• testMethod = "wilcoxon")
  

ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-1239618b28ac0-Date-2023-07-13_Time-16-18-47.log
If there is an issue, please report to github with logFile!
2023-07-13 16:18:47 : Matching Known Biases, 0.006 mins elapsed.
Error in cor(estbgdP, obsbgdP) : incompatible dimensions
In addition: Warning messages:
1: In rbind(estbgd, obsbgd) :
number of columns of result is not a multiple of vector length (arg 1)
2: In rbind(estbgdP, obsbgdP) :
number of columns of result is not a multiple of vector length (arg 1)

class(projmulti_match$cell_annotation)
[1] "character"
ArchR-getMarkerFeatures-1239618b28ac0-Date-2023-07-13_Time-16-18-47.log

[YingxinLin]

Hi, I found using addCellColData to add the clustering results as character vector will solve the problem. Hope it helps!

[CCCCCCheryl]

the problem still remain like the following shows

markersPeaks <- getMarkerFeatures(

• ArchRProj = proj.macs2,

• useMatrix = "PeakMatrix",

• groupBy = "response",

• #bias = c("TSSEnrichment", "log10(nFrags)"),

• testMethod = "wilcoxon"

• )
  ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-99196ed40b42-Date-2023-10-08_Time-23-57-28.log
  If there is an issue, please report to github with logFile!
  2023-10-08 23:57:28 : Matching Known Biases, 0.005 mins elapsed.
  Error in cor(estbgdP, obsbgdP) : incompatible dimensions
  In addition: Warning messages:
  1: In rbind(estbgd, obsbgd) :
  number of columns of result is not a multiple of vector length (arg 1)
  2: In rbind(estbgdP, obsbgdP) :
  number of columns of result is not a multiple of vector length (arg 1)

  any suggestions??

[shycheng]

the problem still remain like the following shows

markersPeaks <- getMarkerFeatures(

• ArchRProj = proj.macs2,
• useMatrix = "PeakMatrix",
• groupBy = "response",
• #bias = c("TSSEnrichment", "log10(nFrags)"),
• testMethod = "wilcoxon"
• )
  ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-99196ed40b42-Date-2023-10-08_Time-23-57-28.log
  If there is an issue, please report to github with logFile!
  2023-10-08 23:57:28 : Matching Known Biases, 0.005 mins elapsed.
  Error in cor(estbgdP, obsbgdP) : incompatible dimensions
  In addition: Warning messages:
  1: In rbind(estbgd, obsbgd) :
  number of columns of result is not a multiple of vector length (arg 1)
  2: In rbind(estbgdP, obsbgdP) :
  number of columns of result is not a multiple of vector length (arg 1)
  any suggestions??

One possible reason is that there are too few cells in some groups. After filtering the group less than 20 cells, it works.