One error when I loading data by using SoupX, Thank you so much.

[MQMQ2018]

Dear Dr. Matthew Young,

It is nice to try to reduce the ambient mRNA in scRNA-seq analysis. I tried to read my 10xgenomics scRNAseq data as below, but encountered an error as below, could you please help to check and give me some tips? Is that because of I loading the folder of aggregated samples by using Cellranger -aggr? Thank you so much.

#===#

dataDirs=c("/scRNAseq/BeforeForceCell/Mixtured/outs")
scl = load10X(dataDirs)
Loading data for 10X channel Channel1 from /scRNAseq/BeforeForceCell/Mixtured/outs
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) :
'NA' indices are not (yet?) supported for sparse Matrices

#===#

Best,
Qi

[shristi-shrestha]

I have the same problem. Did you figure out the fix?

[MQMQ2018]

STill not fully...Wait for author's reply.. Best, Qi

…

On Mon, Feb 25, 2019 at 11:18 AM shr19818 ***@***.***> wrote: I have the same problem. Did you figure out the fix? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ApAOhN7J5znAYR_AHE0bC6qDq0GNaPEWks5vRDbpgaJpZM4aAVOa> .

-- Qi Ma, Postdoctoral Fellow, Bioinformatics, Department of Medicine University of California, San Diego (UCSD) 9500 Gilman Dr. MC0648 La Jolla, CA 92093-0648 (858)5983866 / (858)5346392 maqiwinner@gmail.com q1ma@ucsd.edu

[JonathanCruard]

Hi, I have that problem too, got some clues to resolve this?
Thanks,
JC

[constantAmateur]

This error usually indicates a duplicate or NA row or column name in the sparse matrix. If you have checked your data and are confident this is not the case, please send me an example file and I will investigate further.

[JonathanCruard]

Just saw that you fixed the problem of loading aggregated datasets from cellranger.
By the way thank you for that!
But I noticed that it keep the aggregated samples in the same soup channel. Wouldn't it be better if those aggregated samples were splited into different channels?
Best,
JonathanCruard