giannimonaco
commented
2 years ago Hi,
The method was developed for PBMCs. However, even for PBMC, you might have weird values because of biological or technical variability. It can work for other samples (such as whole blood) and it is normal to get a high percentage of Neutrophils as they constitute about 50-70% of the whole blood. Clearly, it is not possible to have more than 100%, but if you want to compare the amount of neutrophils among the various individuals of your dataset, you could scale the values and just use it as a score.
It would be ideal to use the same processing pipeline used for developing the ABIS method (i.e. kallisto) if you want to have more accurate results (maybe you get better absolute values). However, if you are just looking at the relative comparison between samples, this should not change much if you use TPM values generated using STAR and Stringtie.
Consider also that you might not be able to detect cell types that have very low proportion (such as dentritic cells or plasmablasts). It is already hard to detect them in PBMCs, even worse for whole blood.
On Thu, 17 Feb 2022 at 05:47, padwalmk @.***> wrote:
Hi, I want to use ABIS for deconvolution of the RNA-Seq profiles generated from the whole blood ( only RBCs are removed by RBC lysis buffer) remaining all cells are their. I have run premilinary analysis and finding high Neutorphill percentage ( for some samples greater than 100 %). I am confused that whether ABIS can be used to deconvluate RNA-Seq profiles generated from the whole blood cells. Is this ok to get such a high percentage of the neutrophills in some samples ? Please share your views.
Further, I have generated TPM counts using the "STAR-------> Stringtie" pipeline. Will it be ok or should I generate TPM counts using the salmon pseudoalignments methods as you have suggested in some of your post. ? Thank you..
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padwalmk
Hi, I want to use ABIS for deconvolution of the RNA-Seq profiles generated from the whole blood ( only RBCs are removed by RBC lysis buffer) remaining all cells are their. I have run premilinary analysis and finding high Neutorphill percentage ( for some samples greater than 100 %). I am confused that whether ABIS can be used to deconvluate RNA-Seq profiles generated from the whole blood cells. Is this ok to get such a high percentage of the neutrophills in some samples ? Please share your views.
Further, I have generated TPM counts using the "STAR-------> Stringtie" pipeline. Will it be ok or should I generate TPM counts using the salmon pseudoalignments methods as you have suggested in some of your post. ? Thank you..