Missionbio tapestri : error

[reJELIN]

Hello,

Thanks you for you package !

I'm trying to develop a pipeline of analysis for missionbio multi-omics data. They have something similar to cite-seq but with DNA-seq and protein. So i thought about using your package to normalize my protein read counts.

I used your docker and try to make it work with my data but i'm getting this error :

Error in lnsrch_morph(bvecold, fold, grad, pvec, fngrad_morph, morphList,  : 
  Initial slope not negative.

Perhaps you will have an idea about what i did wrong ?

Thanks you for your time !

[yezhengSTAT]

I think I know where this error is triggered but would you mind sharing the parameters input? Also, does the demo data work on your side?

Thanks, Ye

[reJELIN]

Hello,

thanks you for your answer and time.

this was the paramters input :

cell_x_adt_norm <- ADTnorm(
  cell_x_adt = cell_x_adt, 
  cell_x_feature = cell_x_feature,
  study_name = run_name)

i didn't try the demo to be honest because i'm not really working with cite-seq data even though the methodology for ADT missionbio tapestri pipeline is very similar to cite-seq ADT.

reJELIN

[yezhengSTAT]

Hello, Would you mind giving the demo data a try. The ADT part should be very similar to your data modality. Also, do you mind sharing with me your protein measurement density distribution (very similar to the density track in the vignette). I remember seeing this error before but never run into it again. I suspect that your data may have a little bit different density distribution.

Thanks, Ye