extractSignature non-conformable arrays error

[dschslava]

Dear PoisonAlien,

I tried to run the following command and I got an error message saying that All the runs produced an error.

I got the hg19.fa from UCSC this afternoon.

I can run the following commands with no problem.

plotApobecDiff(tnm = laml.tnm, maf = laml)

Thanks in advance!

laml.sign = extractSignatures(mat = laml.tnm, nTry = 6, plotBestFitRes = FALSE)
Estimating best rank..
Timing stopped at: 0.055 0.001 0.075
Timing stopped at: 1.219 0.015 1.26
Timing stopped at: 0.055 0 0.054
Timing stopped at: 0.629 0.002 0.631
Timing stopped at: 0.011 0 0.012
Timing stopped at: 0.516 0.001 0.516
Timing stopped at: 0.042 0.003 0.044
Timing stopped at: 0.543 0.006 0.544
Timing stopped at: 0.014 0 0.014
Timing stopped at: 0.515 0.003 0.514
Error in (function (...) : All the runs produced an error:
-#1 [r=2] -> non-conformable arrays [in call to '!=']
-#2 [r=3] -> non-conformable arrays [in call to '!=']
-#3 [r=4] -> non-conformable arrays [in call to '!=']
-#4 [r=5] -> non-conformable arrays [in call to '!=']
-#5 [r=6] -> non-conformable arrays [in call to '!=']

[PoisonAlien]

Hello,

Try loading nmf library first and see if it works.

library('NMF')
laml.sign = extractSignatures(mat = laml.tnm, nTry = 6, plotBestFitRes = FALSE)

[dschslava]

Yes I loaded the NMF library first by doing the following:

require('NMF')
laml.sign = extractSignatures(mat = laml.tnm, nTry = 6, plotBestFitRes = FALSE)

I also ran the lamb.tnm = trinucleotideMatrix () command by specifying the file path to hg19 before loading the NMF library and it worked correctly.

Here is my screenshot for the error.

require('NMF')
laml.sign = extractSignatures(mat = laml.tnm, nTry = 6, plotBestFitRes = FALSE)
Estimating best rank..
Timing stopped at: 0.011 0.001 0.021
Timing stopped at: 0.508 0.002 0.518
Timing stopped at: 0.03 0.005 0.036
Timing stopped at: 0.553 0.014 0.572
Timing stopped at: 0.012 0 0.013
Timing stopped at: 0.513 0.003 0.512
Timing stopped at: 0.012 0 0.012
Timing stopped at: 0.528 0.007 0.534
Timing stopped at: 0.011 0.001 0.011
Timing stopped at: 0.528 0.007 0.535
Error in (function (...) : All the runs produced an error:
-#1 [r=2] -> non-conformable arrays [in call to '!=']
-#2 [r=3] -> non-conformable arrays [in call to '!=']
-#3 [r=4] -> non-conformable arrays [in call to '!=']
-#4 [r=5] -> non-conformable arrays [in call to '!=']
-#5 [r=6] -> non-conformable arrays [in call to '!=']

[PoisonAlien]

Hi,
How many samples do you have ? and whats the mutations rate per sample ?

[dschslava]

Here is the sample size information:
$SampleSummary
Cohort SampleSize
1: Enriched 4
2: nonEnriched 172

getSampleSummary(laml)
Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins Missense_Mutation Nonsense_Mutation Splice_Site total
1: TCGA-AB-3009 0 5 0 1 25 2 1 34
2: TCGA-AB-2807 1 0 1 0 16 3 4 25
3: TCGA-AB-2959 0 0 0 0 22 0 1 23
4: TCGA-AB-3002 0 0 0 0 15 1 5 21
5: TCGA-AB-2849 0 1 0 0 16 1 2 20

---

188: TCGA-AB-2933 0 0 0 0 1 0 0 1
189: TCGA-AB-2942 0 0 0 1 0 0 0 1
190: TCGA-AB-2946 0 0 0 0 1 0 0 1
191: TCGA-AB-2954 0 0 0 0 1 0 0 1
192: TCGA-AB-2982 0 0 0 0 1 0 0 1

[dschslava]

Here is where the hp19.fa is located:
https://drive.google.com/open?id=19ZVaNWzOXebaxE5OY24WWZKtQMHcAAwc

Please let me know if you need permission to download.

[WatsonCrick2018]

Could you share with me where your hg19.fa is located so I can try it out?

[PoisonAlien]

@dschslava Hi,
Can you upload your tnm matrix here ? You can write it to a tsv file and attach it here..

write.table(laml$nmf_matrix, "tnm.tsv", sep = "\t", quote = FALSE)

Keep rownames.

[dschslava]

Dear PoisonAlien,

Thank you for the instruction. I got the following error:

write.table(laml$nmf_matrix, "tnm.tsv", sep = "\t", quote = FALSE)
Error in laml$nmf_matrix : $ operator not defined for this S4 class

[PoisonAlien]

Oh, Sorry my mistake.
Try this laml.tnm$nmf_matrix

[dschslava]

Dear PoisonAlien,

This time it worked but I don't know where to find tam.tsv file. It is not in extdata.

write.table(laml.tnm$nmf_matrix, "tnm.tsv", sep = "\t", quote = FALSE)

Thanks!

[dschslava]

Sorry, I don't know how to attach an file in GitHub. Here you go. Please let me know the path to your hg19.fa file so I can verify on my side. Thanks, Stephen Canyon Crest Academy High School San Diego, CA

…

On Tue, Feb 6, 2018 at 11:28 PM, PoisonAlien ***@***.***> wrote: Oh, Sorry my mistake. Try this laml.tnm$nmf_matrix — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#119 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYToF9Y1K-z0zmWUghpbRjWmrllgQIkUks5tSVC0gaJpZM4R1F3N> .

-- Stephen