Error on runspatialdecon and spatialdecon - Only 3 genes are shared between norm and X - this may not be enough to support accurate deconvolution

[borexino]

I'm trying to perform SpatialDecon on GeoMX DSP data prior filtered following the NanoString R guide .

For runspatialdeconI'm using code from here:

res = runspatialdecon(object = target_demoData,     # My S4 obj
                      norm_elt = "q_norm",          # Referring to Q3 norm for WTA/CTA  w/ or w/o custom spike-ins. As suggested by the above mentioned guide
                      raw_elt = "exprs",            # Raw exprs
                      X = safeTME,
                      align_genes = TRUE)

I get this:

In addition, I tried spatialdecon following the code from here :

res = spatialdecon(norm = norm,
                   bg = bg,
                   X = safeTME,
                   align_genes = TRUE)

Output:

head(bg)

Can someone help?

[maddygriz]

Hi @borexino,

Thank you for reaching out. Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Quick look, it looks like you are running mouse data but safeTME is a human profile matrix. We do not have a mouse equivalent to safeTME but this ImmGen Immune Atlas profile might be the best substitute.

Thanks,
Maddy

[borexino]

Thanks @maddygriz!!
What about mini_singleCell_dataset ? Is this ok for mice?
Thanks

[maddygriz]

The mini_singleCell_dataset is also human but we have all of these mouse profiles to choose from.

[borexino]

Could you suggest what to use for mouse small intenstine? I've this situation now

mouseintestine <- download_profile_matrix(species = "Mouse",
                                       age_group = "Adult", 
                                       matrixname = "SmallIntestine_MCA")

[maddygriz]

I am not an expert on the contents of each profile. Each matrix has the metadata located here for users to determine the best dataset for their study.