Low level of Neutrophils in PBMC

dviraran / xCell

Cell types enrichment analysis

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Low level of Neutrophils in PBMC #25

Open antgomo opened 5 years ago

antgomo commented 5 years ago

I am using xCell on PBMC RNAseq data

I am using counts per miilion TMM normalized, the main thing is surpringsly, at the levels of Neutrophils is very low if not, completely absent

I use your example data analyzed as microarray and i found exactly the same. Is it correct? I mean, i expected a high levels of neutrophils due to the fact that they are highly present on PBMC

Thanks in advance

dviraran commented 5 years ago

Hi,

You have your facts wrong. Neutrophils are PMNs, and are removed in PBMC.

Best, Dvir

antgomo commented 5 years ago

Sorry, i didn't explain myself clearly

Ok, so according your data everything is OK, my data is whole blodd and i found that neutrophils are gone, unless i don't understand the biology behind, the neutrophils must be there, am i right?

Maybe i have to log the data before to use your alogorihm?

dviraran commented 5 years ago

Well, if you are using whole blood than definitely, you should see neutrophils. In my experience, xCell was able to detect neutrophils, so I don't know why it is failing in your data.

Not sure what you mean by log the data.