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Teichlab / cellphonedb

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Issue with Invalid Counts Data #203

Closed SaskiaFreytag closed 3 years ago

SaskiaFreytag commented 4 years ago

Hi,

I have been trying to run CellPhoneDB on my own data but kept getting Invalid Counts Error. I then switched to your test data and obtained the same data. I have even installed it in an environment as suggested but it would not change the result.

Any help would be much appreciated!

mief commented 3 years ago

Hi, Can you send us a sample of your input data and we can try to test it? Thanks!

Portulaca666 commented 3 years ago

Counts values are not decimal values image Who can help me ! please !

prete commented 3 years ago

Hi @wuzhigui can you provide a sample of your input data that we can use to reproduce your error?

prete commented 3 years ago

@wuzhigui your counts file probably had the wrong format. Were you able to run your analysis?

Portulaca666 commented 3 years ago

thanks , i have solved this error.

---Original--- From: @.> Date: Fri, May 7, 2021 20:25 PM To: @.>; Cc: @.**@.>; Subject: Re: [Teichlab/cellphonedb] Issue with Invalid Counts Data (#203)

@wuzhigui your counts file probably had the wrong format. Were you able to run your analysis?

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prete commented 3 years ago

@SaskiaFreytag this is probably too late, but did you too manage to run your analysis?

Portulaca666 commented 3 years ago

yes

---Original--- From: @.> Date: Fri, May 7, 2021 20:32 PM To: @.>; Cc: @.**@.>; Subject: Re: [Teichlab/cellphonedb] Issue with Invalid Counts Data (#203)

@SaskiaFreytag this is probably too late, but did you too manage to run your analysis?

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prete commented 3 years ago

yes

Thanks wuzhigui, but I was asking the original reporter of the issue (@SaskiaFreytag) that second time. I'll give them some time to check-in and then I'll close the issue.

monikaramos commented 2 years ago

Hi. I am having this same error. Can someone provide an explanation?

xiaoxiaofuyou commented 2 years ago

Oh, who can help me to solve this problem, i got the same error, thank you!

image

Best to all of you.

Portulaca666 commented 2 years ago

It is very explicit that you should use Symbol gene type .

---Original--- From: @.> Date: Thu, Jun 23, 2022 17:16 PM To: @.>; Cc: @.**@.>; Subject: Re: [Teichlab/cellphonedb] Issue with Invalid Counts Data (#203)

Oh, who can help me to solve this problem, i got the same error, thank you!

Best to all of you.

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prete commented 2 years ago

Hi @xiaoxiaofuyou as wuzigui mentioned there's a WARNING with a pretty explicit message. It says that your data is not using enembl gene names. You should run your command with the option --counts-data hgnc_symbol if you're using gene names instead of ensembl gene identifiers.

Should that not work you may want to have a second look at the format of your data. Are they valid tab or comma separated values? Perhaps you can provide the files you're trying to use so we can give you better guidance.

xiaoxiaofuyou commented 2 years ago

Thank you. I solved it by adding a code. mycounts <- as.matrix(mycounts)