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lung12.expr
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I am receiving the following error from the fitPoisthNorm() function.
probe finished
Error in solve.default(cov_mat) :
system is computationally singular: reciprocal condition number = 1.04181…
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I received raw counts and normalized GeoMX data. The raw counts data contain multiple negative probes (negprobe-WTX). Do I need to compute the geometric mean of these negative probes in the raw counts…
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Hi Nanostring Team,
our working group is currently looking into this package of yours. We are trying to reproduce figures from the nature paper "Advances in mixed cell deconvolution enable quantifi…
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Hi,
We have tried using Q3 and TMM normalisation for DSP WTA data. But when it comes to TCR spike-in add-on data, which normalisation methods (Q3, TMM or Poisson threshold model based normalisati…
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Hi, I don't see any specification of processing WTA or CTA data using this package. I only see a WTA workflow. Not sure if there is somewhere need to be taken care of on CTA data different from WTA. C…
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Hi,
I'm having an issue when I run the spatialdecon() function on my dataset with the downloaded ImmuneCensus_HCA profile matrix. I have around 2500 genes for around 12 samples in my dataset which …
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Hi,
thank you for this useful package.
Can you suggest how to generate UMAP or tSNE from a`reverseDecon`object?
Thanks
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Hello,
while running the spatialdecon function I have been receiving error messages Warning NaNs produced, Warning Unsuccessful Convergence. What leads to the production of NaNs. I underst…
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Hello,
I have some GeoMX WTA data, but I was wondering if there was a possibility of normalizing the matrix just from the count matrix? Also I was wondering what do we do if we have multiple negati…