giannimonaco
commented
1 year ago Dear Philipp,
thank you for checking out on ABIS and for building up on it!
The scaling factor that I used to normalize the TPM values for mRNA abundance are in the attached file. For each immune cell type you can multiply the corresponding scaling factor.
Also, consider that the ABIS-Seq signature matrix in Table S5 ( https://www.cell.com/cms/10.1016/j.celrep.2019.01.041/attachment/26489ab2-3c33-42ee-9ca0-23c76eec45b4/mmc6.xlsx) is already normalized by mRNA abundance.
Best wishes, Gianni
On Fri, Mar 17, 2023 at 11:21 AM pippomz @.***> wrote:
Hello,
thank you fpr the amazing work on ABIS!
I was wondering how you obtained the TPM values scaled by mRNA abundance with RLM like you did in the original publication, https://www.cell.com/cell-reports/pdf/S2211-1247(19)30059-2.pdf Figure 7B.
In particular, I would like to test to input your signature matrix, scaled by mRNA abundance, into other deconvolution methods like FARDEEP.
The aim is forcing the cell populations to a positive scale (i.e., no negetaive values and 0 as the lower boundary).
Thank you, Philipp
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"Monocytes C" 1.60188683963836 "NK" 0.749021326878403 "T CD8 Memory" 0.680038733676581 "T CD4 Naive" 0.803789736569463 "T CD8 Naive" 0.554283071383344 "B Naive" 0.830474573526442 "T CD4 Memory" 0.915518848522562 "MAIT" 0.586886579159884 "T gd Vd2" 0.978694612616693 "Neutrophils LD" 0.591354344063847 "T gd non-Vd2" 0.794170174589765 "Basophils LD" 0.468297600598404 "Monocytes NC+I" 1.69412826660189 "B Memory" 0.876070158504131 "mDCs" 4.98460363063607 "pDCs" 1.40380514821998 "Plasmablasts" 9.120624594303 "Progenitors" 5.04575898035311
Hello,
thank you fpr the amazing work on ABIS!
I was wondering how you obtained the TPM values scaled by mRNA abundance with RLM like you did in the original publication, Figure 7B.
In particular, I would like to test to input your signature matrix, scaled by mRNA abundance, into other deconvolution methods like FARDEEP.
The aim is forcing the cell populations to a positive scale (i.e., no negetaive values and 0 as the lower boundary).
Thank you, Philipp