How to focus on a specific class of molecules

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Marco Fidaleo

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May 1, 2024, 1:42:13 PMMay 1
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Hello everyone,

I am conducting a clustering analysis using the Classification with Spatial Shrunken Centroids (SSC) method. My sample consists of nervous tissue and is therefore highly characterized by lipids. When I apply SSC, I can identify clusters that are characterized by m/z ions that likely belong to the lipid class. Furthermore, when I examine which ions have contributed to a specific cluster, it seems to me that the same ions have contributed to multiple clusters and, in any case (at least with my datasets), I cannot find a cluster mostly described by one ion. Here is an example:

> topFeatures(mse_tot_ssc_mean, model=list(r=2, s=0), class==1) Top-ranked features: mz r k s class centers statistic 1 888.6329 2 20 0 1 7360.356 288.8289 2 889.6364 2 20 0 1 3918.336 271.9897 3 890.6475 2 20 0 1 8066.914 268.1355 4 892.6499 2 20 0 1 2587.962 252.9644 5 891.6520 2 20 0 1 4109.068 251.9183 6 862.6159 2 20 0 1 2478.923 245.5485 7 878.6146 2 20 0 1 2233.640 235.3656 8 906.6454 2 20 0 1 2822.483 233.3550 9 864.6236 2 20 0 1 1192.637 230.4855 10 863.6157 2 20 0 1 1514.358 226.4598 > topFeatures(mse_tot_ssc_mean, model=list(r=2, s=0), class==2) Top-ranked features: mz r k s class centers statistic 1 890.6475 2 20 0 2 7667.4032 188.5471 2 891.6520 2 20 0 2 3926.4879 179.7538 3 888.6329 2 20 0 2 6588.2490 174.5789 4 726.5536 2 20 0 2 5242.1476 172.0922 5 462.3054 2 20 0 2 817.5346 169.2137 6 892.6499 2 20 0 2 2408.9569 168.1051 7 889.6364 2 20 0 2 3524.6678 165.9360 8 727.5567 2 20 0 2 2484.8955 161.3878 9 862.6159 2 20 0 2 2275.3719 155.9419 10 744.5618 2 20 0 2 1017.0777 144.2835

I believe that in my case, a specific cluster is defined by the co-presence of two or more ions. Although, this type of result does not allow me to identify a specific ion that can describe the cluster. I can conclude that several ions determine a specific cluster. Am I right?

Additionally, I would like to exclude lipids from my clustering analysis. How can I do this? I suppose instead of considering all ions, I can selectively analyze only a portion of the spectrum and then conduct the clustering analysis on the specific portion. When I analyze the entire dataset with the function summarizeFeatures, I tried several modes (mean, min, max), but I obtained more or less the same ions in the specific cluster. So, if I read only a portion of the spectrum, could I obtain reliable results or could I generate artifacts? Are there other methods to exclude classes of molecules?

Thanks in advance,

M


kbemis

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May 2, 2024, 12:43:41 PMMay 2
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You are using s=0, so there is no sparsity enforced, so all clusters will be informed by all ions. Set s > 0 to enforce sparsity. Higher values of s will use fewer ions.

To exclude ions from the analysis, you would subset the dataset before giving it to the statistical method.

You can use subsetFeatures() to create a subset of the dataset with a certain mass range.

-Kylie

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