Handle older assay IDs

[andrewrech]

Please add the following

  # Handle older assay probe labels
  if (pkcData[["RTS_ID"]][1] %like% "^RTS" &
    probeAssay[["RTS_ID"]][1] %like% "^RNA") {
    # replace RTS00 with RNA in probeAssay[["RTS_ID"]]
    probeAssay[["RTS_ID"]] <- gsub("^RNA", "RTS00", probeAssay[["RTS_ID"]])
  }

https://github.com/andrewrech/GeomxTools/commit/d567c3590cffc1afd8387e09d55a0a3942b33780

to handle assays that use the older probe labels.

thanks

Andrew

[maddygriz]

Hi Andrew,

Thanks for this fix, we will consider this for the next release.
What PKC are you using so we can make sure future GeomxTools releases are fully compatible with legacy files still in use?

Maddy

[andrewrech]

This is from 2021 datasetthat is used in a package test for my internal tool. The PKC file is GeoMx_Hs_CTA_v1.0.pkc, which has the newer labels. The DCC files are I think TAP program generated and have the older RNA* labels.

[maddygriz]

Gotcha. So older DCC files and a newer PKC file. I will add that to our internal bug so we can test the correct situation.

Thanks,
Maddy

[shaniAmare]

Has this been fixed? I get the following error when I try the Mm_R_NGS_WTA_v1.0.pkc which I'm assuming is due to incompatibility of pic file and the dcc files.

Error in data.frame(RTS_ID = pkcData[zeroProbes, "RTS_ID"], Count = rep(0,  : 
  arguments imply differing number of rows: 20175, 0

The code I'm trying is:

> dccSet <-
+     suppressWarnings(readNanoStringGeoMxSet(dccFiles = dccFiles,
+                            pkcFiles = PKCFiles,
+                            phenoDataFile = SampleAnnotationFile,
+                            phenoDataSheet = "SegmentProperties",
+                            phenoDataDccColName = "SegmentDisplayName"))

Many thanks for your time
Shani.

[maddygriz]

Hi @shaniAmare,

Yours might be a different issue. Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks,
Maddy