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lengning / OEFinder

Identify ordering effect genes in single cell RNA-seq data
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Error message #1

Open jhsiao999 opened 9 years ago

jhsiao999 commented 9 years ago

Hi,

First of all, thank you for pointing out the ordering effect of capture sites. As a result, we are now beginning to explore this issue in our data. I recently encountered an error message while running OEFinder. I wonder if you can help me to decipher this message...

Warning in summary.lm(aa) : essentially perfect fit: summary may be unreliable

Best, Joyce Hsiao

Postdoctoral fellow at University of Chicago

lengning commented 9 years ago

Hi Joyce, Thanks for your interests in OEFinder! Seems to me this warning message means that one of the genes gave a perfect fitting (RSS=0) in the spline fitting step. Then the summary statistics might be not very accurate. I wouldn't worry about this too much since the OEFinder calls OE genes based on permutation results. Let me know if you have any other questions. Best, Ning

On Sat, Sep 26, 2015 at 9:26 PM, Chiaowen Joyce Hsiao < notifications@github.com> wrote:

Hi,

First of all, thank you for pointing out the ordering effect of capture sites. As a result, we are now beginning to explore this issue in our data. I recently encountered an error message while running OEFinder. I wonder if you can help me to decipher this message...

Warning in summary.lm(aa) : essentially perfect fit: summary may be unreliable

Best, Joyce Hsiao

Postdoctoral fellow at University of Chicago

— Reply to this email directly or view it on GitHub https://github.com/lengning/OEFinder/issues/1.

Ning Leng, Ph.D Computational Biologist / Biostatistician Regenerative Biology Laboratory Morgridge Institute for Research

jhsiao999 commented 9 years ago

Hi Ning,

Thanks for the quick reply. I finally get a chance to re-run the OEFinder again. Below is the complete error message:

Warning in summary.lm(aa) : essentially perfect fit: summary may be unreliable Error in Datasort[, sample(1:Ncol, Ncol)] : subscript out of bounds Error in Datasort[, sample(1:Ncol, Ncol)] : subscript out of bounds

I waited for a few minutes to see if the program would still generate output files, and it didn't.

One thing to note is that the OEFinder ran perfectly okay when I combined data from 9 plates. However, the error messages came up when I ran on data from 1 plate or data from 3 plates combined together.

Any help with this is greatly appreciated. Thanks!

Joyce Hsiao

lengning commented 9 years ago

Hi Chiaowen, Would you mind to send me an example input that generates this bug for further debugging? Thanks, Ning

On Fri, Oct 2, 2015 at 5:10 PM, Chiaowen Joyce Hsiao < notifications@github.com> wrote:

Hi Ning,

Thanks for the quick reply. I finally get a chance to re-run the OEFinder again. Below is the complete error message:

Warning in summary.lm(aa) : essentially perfect fit: summary may be unreliable Error in Datasort[, sample(1:Ncol, Ncol)] : subscript out of bounds Error in Datasort[, sample(1:Ncol, Ncol)] : subscript out of bounds

I waited for a few minutes to see if the program would still generate output files, and it didn't.

One thing to note is that the OEFinder ran perfectly okay when I combined data from 9 plates. However, the error messages came up when I ran on data from 1 plate or data from 3 plates combined together.

Any help with this is greatly appreciated. Thanks!

Joyce Hsiao

— Reply to this email directly or view it on GitHub https://github.com/lengning/OEFinder/issues/1#issuecomment-145156091.

Ning Leng, Ph.D Computational Biologist / Biostatistician Regenerative Biology Laboratory Morgridge Institute for Research