<div dir="ltr"><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Renaud Gaujoux</b> <span dir="ltr"><<a href="mailto:renaud@cbio.uct.ac.za">renaud@cbio.uct.ac.za</a>></span><br>
Date: 26 May 2014 10:24<br>Subject: Re: [NMF-user] matrix size limit?<br>To: Thomas Tibbitts <<a href="mailto:Thomas.Tibbitts@infi.com">Thomas.Tibbitts@infi.com</a>><br><br><br>Are you sure you are reading the data correctly? The names seem strange.<br>

<div class="HOEnZb"><div class="h5"><br>
<br>
On 23 May 2014 22:28, Thomas Tibbitts <<a href="mailto:Thomas.Tibbitts@infi.com">Thomas.Tibbitts@infi.com</a>> wrote:<br>
> Hi Renaud,<br>
><br>
> Thank you for your quick response.<br>
><br>
> This test returns TRUE:<br>
> min(rowSums(x, na.rm = TRUE), na.rm = TRUE) == 0<br>
> [1] TRUE<br>
><br>
> Then I received the following output with the next two commands:<br>
> s <- rowSums(x, na.rm = TRUE)<br>
> str(which(<a href="http://is.na" target="_blank">is.na</a>(s) | s==0))<br>
>  Named int [1:1691] 1 2 3 4 5 6 7 8 9 10 ...<br>
>  - attr(*, "names")= chr [1:1691] "ABCA13_11152_A2223P,0,0,0,0,0,0,0.46,0.5,0.53,0.51,0,0,0,0,0,0,0,0,0.48,0.45,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.47,0.46,0,0,0,0,0.48"| __truncated__ "ABCA13_11157_K2306T,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0"| __truncated__ "ABCA13_11161_S2537A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.5,0.5,0,0"| __truncated__ "ABCA13_11163_D2630G,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0"| __truncated__ ...<br>

><br>
> After the header row, the first few lines of the data in my file are:<br>
> ABCA13_11152_A2223P,0,0,0,0,0,0,0.46,0.5,0.53,0.51,0,0,0,0,0,0,0,0,0.48,0.45,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.47,0.46,0,0,0,0,0.48,0.48,0,0,0,0,0.47,0.53,0,0,0,0,0,0,0,0,0,0,0,0,0,0.56,0,0,0.5,0.48,0,0,0,0,0,0,0,0,0.48,0.46,0.45,0.47,0,0,0,0,0,0,0,0,0,0,0,0,0,0<br>

> ABCA13_11157_K2306T,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.48,0.5,0,0,0,0,0,0,0,0,0,0,0.54,0.48,0,0,0,0,0,0,0,0<br>

> ABCA13_11161_S2537A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.5,0.5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.48,0.48,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0<br>

> ABCA13_11163_D2630G,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.47,0.48,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0<br>
><br>
> So the error message did not help. Do you have any other ideas?<br>
> I am not sure how to turn on logging in R to get a complete log.<br>
><br>
> Thank you again for your help!<br>
> Best regards,<br>
> Tom<br>
><br>
> -----Original Message-----<br>
> From: <a href="mailto:getoxxx@gmail.com">getoxxx@gmail.com</a> [mailto:<a href="mailto:getoxxx@gmail.com">getoxxx@gmail.com</a>] On Behalf Of Renaud Gaujoux<br>
> Sent: Monday, May 19, 2014 4:58 PM<br>
> To: Thomas Tibbitts<br>
> Cc: <a href="mailto:nmf-user@lists.r-forge.r-project.org">nmf-user@lists.r-forge.r-project.org</a><br>
> Subject: Re: [NMF-user] matrix size limit?<br>
><br>
> Hi Thomas,<br>
><br>
> this is not really a large matrix and should not pose a problem, for example on a toy dataset:<br>
><br>
>> x <- rmatrix(4000, 100)<br>
>> res <- nmf(x, 3)<br>
>> runtime(res)<br>
>    user  system elapsed<br>
>  19.888   0.004  19.899<br>
>> res <- nmf(x, 3, nrun = 3)<br>
>> runtime(res)<br>
>    user  system elapsed<br>
>  33.262   0.004  33.447<br>
>><br>
><br>
> Do you see warnings as well? Sending a complete log would help.<br>
> The error you see is thrown if the following test is TRUE:<br>
><br>
> min(rowSums(x, na.rm = TRUE), na.rm = TRUE) == 0<br>
><br>
> Can you please directly run this test on your data? It should return TRUE. Then look at:<br>
><br>
> s <- rowSums(x, na.rm = TRUE)<br>
> str(which( <a href="http://is.na" target="_blank">is.na</a>(s) | s == 0 ))<br>
><br>
> which will give you a hint on which row(s) are detected as problematic. By the way, is your dataset nonnegative?<br>
><br>
> Bests,<br>
> Renaud<br>
><br>
> On 19 May 2014 18:37, Thomas Tibbitts <<a href="mailto:Thomas.Tibbitts@infi.com">Thomas.Tibbitts@infi.com</a>> wrote:<br>
>> NMF-users,<br>
>><br>
>><br>
>><br>
>> I can run NMF with a matrix of 1646 rows x 100 columns without error.<br>
>><br>
>><br>
>><br>
>> However when I combine data sets into a larger matrix of 3495 rows x<br>
>> 100 columns I keep getting the error:<br>
>><br>
>> Error:  NMF::nmf  – Input matrix x contains at least one null or<br>
>> NA-filled row.<br>
>><br>
>><br>
>><br>
>> There are no nulls or NA-filled rows in the larger matrix, I wrote it<br>
>> out to disk to make sure.<br>
>><br>
>><br>
>><br>
>> So I ‘m thinking I hit an matrix size limitation.<br>
>><br>
>> How can I fix this problem?<br>
>><br>
>><br>
>><br>
>> Thank you.<br>
>><br>
>> Tom<br>
>><br>
>> This message and any attachments may contain confidential information<br>
>> and/or privileged material. If you received this message in error,<br>
>> please contact the sender and delete this message and any attachments<br>
>> immediately. Thank you.<br>
>><br>
>> _______________________________________________<br>
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>><br>
>><br>
><br>
><br>
><br>
> --<br>
> Renaud Gaujoux, PhD<br>
> Systems Immunology - Technion, Haifa, Israel<br>
> This message and any attachments may contain confidential information and/or privileged material. If you received this message in error, please contact the sender and delete this message and any attachments immediately. Thank you.<br>

<br>
<br>
<br>
--<br>
Renaud Gaujoux, PhD<br>
Systems Immunology - Technion, Haifa, Israel<br>
</div></div></div><br><br clear="all"><br>-- <br><div dir="ltr"><div><div><font><span style="font-family:arial,helvetica,sans-serif">Renaud Gaujoux, PhD<br></span></font></div><font><span style="font-family:arial,helvetica,sans-serif">Systems Immunology - Technion, Haifa, Israel<br>
</span></font></div><font><span style="font-family:arial,helvetica,sans-serif"></span></font><div><font><br></font></div></div>
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