Open andrewrech opened 1 year ago
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
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.
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
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.
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
Please add the following
https://github.com/andrewrech/GeomxTools/commit/d567c3590cffc1afd8387e09d55a0a3942b33780
to handle assays that use the older probe labels.
thanks
Andrew