Question

GISTIC 2.0.23 error

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7.5 years ago

mkaushal ▴ 120

Hi,

I am trying to run GISTIC analysis for 30 metastasized sample data. I ran Varscan copy number and DNACopy and made my segmentation file. When I run GISTIC I get this error:

GISTIC version 2.0.23

GISTIC 2.0 input error detected: All input data were removed after NaN processing

I guess GISTIC needs to have overlapping regions where all 30 samples share results. I found a region in chr 11 with 27 samples sharing the data. To test this I incorporated 3 toy segments for 3 missing samples for this region and ran GISTIC again.I get this error now:

GISTIC version 2.0.23 Warning: Number of markers is less than smooth length for the following chromosomes: 11. These chromosomes will not be smoothed. (Smooth length = 8.)

In smooth_cbs at 54

In clean_gistic_input at 77

In run_gistic2_from_seg at 238

In gp_gistic2_from_seg at 97

Index exceeds matrix dimensions.

Error in normalize_by_arm_length (line 85)

Error in make_sample_B (line 50)

Error in perform_deconstruction (line 68)

I am clearly doing something wrong in incorporating toy segments. I also know this is not the best workaround. So any pointers will really help me. Thanks

gistic dnacopy copy number • 9.5k views

ADD COMMENT • link updated 2.0 years ago by xingyu ▴ 10 • written 7.5 years ago by mkaushal ▴ 120

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Hi, i came across the same problem and wonder if you have solved it yet. Could you please give me your email address so that i can contact you for further information, or you may email me at <email address censored>. Thanks in advance.

ADD REPLY • link updated 6.7 years ago by WouterDeCoster 47k • written 7.0 years ago by iiii_hr ▴ 10

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For anyone still struggling with this error - I had removed the sex chromsomes at an earlier point of the analysis. Whilst it seemed I had at least some coverage in all samples there was obviously none in Chr23, causing the error.

Be sure to plot your segments per-sample, per-chromosome to ensure you have no gaps.

ADD REPLY • link 5.5 years ago by dompearcejankowski ▴ 10

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Hi, i got the same error ,have you solved the problem? could you tell me ? tanks in advance

ADD REPLY • link 6.7 years ago by 498476732 • 0

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hi, have you solved your problem? I have the same issue

ADD REPLY • link 6.7 years ago by tianshizuolu • 0

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See the comment below.

ADD REPLY • link 6.7 years ago by mkaushal ▴ 120

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Have you solved your problem? I have the same issue

ADD REPLY • link 6.3 years ago by huang182 • 0

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2.0 years ago

xingyu ▴ 10

I met this problem, too. Is there a particular processing procedure?

ADD COMMENT • link 2.0 years ago by xingyu ▴ 10

score 2 · Accepted Answer · 2018-03-21

This is the reply I obtained in the gistic google forum:

Hi Madhu,

As you correctly guessed, GISTIC only works with regions that are covered by segments across all samples. The "NaN processing" removes regions that have a gap in one or more samples, which in your case is all of your data. The warning message you got when you added in toy segments is telling you that the number of markers with complete data was smaller tha the join segment size, however the error was caused by having no data on chromosomes 1-10: GISTIC requires that all chromosomes have at least some data.

The underlying problem is that you don't have very complete data. Is it possible that your segmentation procedure only creates segments for non-neutral copy number?

Best, Steve