constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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One error when I loading data by using SoupX, Thank you so much. #8

Closed MQMQ2018 closed 5 years ago

MQMQ2018 commented 5 years ago

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.

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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

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Best, Qi

shristi-shrestha commented 5 years ago

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

MQMQ2018 commented 5 years ago

STill not fully...Wait for author's reply..

Best, Qi

On Mon, Feb 25, 2019 at 11:18 AM shr19818 notifications@github.com 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 https://github.com/constantAmateur/SoupX/issues/8#issuecomment-467144045, 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 commented 5 years ago

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

constantAmateur commented 5 years ago

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 commented 5 years ago

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