SpatialDecon using readGeoMx

[jjoo12]

Hello,

I am a student currently analyzing GeoMx data using StandR. I am in the process of learning spatial analysis and encountered a specific issue, so I decided to reach out on GitHub.

When creating spatial experiment data using the readGeoMx function, there were no issues following the default flow, where rmNegProbe is carried out. However, when attempting spatial deconvolution with rmNegProbe set to FALSE, I am encountering a duplicate error. I suspect this might be related to the usage of WTA data.(There are 139 NegProbe-WTX) How is this typically resolved in such situations?

Thank you!

This is the error code

Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique value when setting 'row.names': ‘NegProbe-WTX’

Thank you

[hookoop]

We are getting the following error: "NegProbe-WTXmust be included in the dataset. Perhaps specify rmNegProbe=TRUE when using readGeoMx" when using prepareSpatialDecon. We are using WTA so there are several negative probes, however we do not understand what the pool= variable in the command should look like. The vignette says "A vector indicates the pools of the genes.", but what does this mean? A vector of gene names?

Best, Helka

[ningbioinfo]

hi @hookoop , the input for the pool argument is a vector with length of the genes, i.e. nrow(spe). It should be something like c("negprob1","negprob1","negprob1","negprob2","negprob2","negprob2"..., "negprobx"), so it tells the function with negative probes is governing which genes.

[ningbioinfo]

hi @jjoo12 , what you need to do is first change the name of the negprobe-wtx into maybe negprobe-wtx1,negprobe-wtx2,negprobe-wtx3,..., negprobe-wtx139. Then use the pool argument in the function to specify which negprobe is responsible for which gene

[hookoop]

Hey @ningbioinfo , how do we find out which negative probe is assigned to which gene? We couldn't figure this out based off the file we got from GeoMX data analysis suite

[ningbioinfo]

Hi @hookoop , I think that's a question for people who run the experiment then.

[hookoop]

Hi @ningbioinfo , we ran the experiment ourselves. @jjoo12 were you able to get prepareSpatialDecon to work with the WTA?

[ningbioinfo]

Hi @hookoop , I see, it should be related to the probe designed etc. I wrote this function based on what they required for the spatialDecon package, which is the tool from the Nanostring company, perhaps send through a question to the company for enquiry the relevant information?