GeoMX protein data

[jiangzh-coder]

i need test GeoMX protein data, and got following errors:

countFile.txt


sampleAnnoFile.txt


featureAnnoFile.txt

spe22 <- readGeoMx("./countFile.txt",

•                "./sampleAnnoFile.txt", 
  

•                "./featureAnnoFile.txt") #,hasNegProbe = TRUE
  

New names:
• `` -> ...1
Rows: 33 Columns: 16384
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (1): TargetName
dbl (16383): ...1, c_1_100_1, c_1_100_10, c_1_100_100, c_1_100_1000, c_1_100_1001, c_1_100_1002, c_1_100_1003, c_1...

ℹ Use spec() to retrieve the full column specification for this data.
ℹ Specify the column types or set show_col_types = FALSE to quiet this message.
Error in geomx_import_fun(countFile, sampleAnnoFile, featureAnnoFile, :
NegProbeName is not found in your count file.

[ningbioinfo]

Hi @jiangzh-coder , your error message tells that the default negative probe name is not found, I'm assuming the "Negative" is the negative marker in your data, if you want to remove it, you can add NegProbeName = "Negative", or if you want to keep it you can set hasNegProbe = FALSE, this should fix up the error.

However, I also spotted that in your samleAnnoFile, the column name of the sample names is something weird, like "row.names(sample_data*)", I would change it to "SegmentDisplayName" as it's the default name the function is trying to look for.