ChIPQC error: Error in generating sample data
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Entering edit mode
meeta.mistry ▴ 20
@meetamistry-7355
Last seen 6 weeks ago
United States

Hello,

I have vehemently searched the Bioconductor support site for answers with no success, and hoping someone might be able to help me. I am running ChIPQC on fission yeast samples and while it gets through most of the samples when generating the object, I can't get past a certain point.

The error is listed below (out of bound indices and out of bound ranges), and I have no idea how to troubleshoot but I have some thoughts on why this might be happening.

1. I have tried running it with consensus = T and consensus =F, but still get the same error.

2. I do not have an annotation file and am wondering if this is the root of the problem?

3. I have tried with and without columns for the bamControl and ControlID in my samples.csv file (as shown in the help ?ChIPQC), although the tutorial example does not have these columns. Is it recommended to have input file information?

3. When I load these same samples into DifffBind I am able to conduct the analyses just fine. Using DiffBind I see that the samples that are throwing an error, are those that have low FrIP (5-10%). Perhaps this is the problem?

Any help with this would be great and much appreciated!

Many thanks,

Meeta

chipQC <- ChIPQC(experiment=samples, consensus = TRUE,
chromosomes=c('AB325691ASM294v2', 'IASM294v2','IIASM294v2',               'IIIASM294v2','MTASM294v2', 'MTRASM294v2'))


Error in sample WT-0h-replicate2: subscript contains NAs or out-of-bounds indices
Error in sample WT-0h-replicate3: subscript contains NAs or out-of-bounds indices
Error in sample WT-0h-replicate4: subscript contains NAs or out-of-bounds indices
Error in sample WT-24h-replicate4: subscript contains NAs or out-of-bounds indices
Error in sample sample43_S43_combined: subscript contains out-of-bounds ranges
Error in sample chipseq41_S41_combined: subscript contains out-of-bounds ranges
Error in ChIPQC(experiment = samples, consensus = TRUE, chromosomes = c("AB325691ASM294v2",  :

Errors in generating sample data.
In addition: Warning messages:
1: In if (class(sample) != "ChIPQCsample") { :
the condition has length > 1 and only the first element will be used
2: In if (class(sample) != "ChIPQCsample") { :
the condition has length > 1 and only the first element will be used
3: In if (class(sample) != "ChIPQCsample") { :
the condition has length > 1 and only the first element will be used
4: In if (class(sample) != "ChIPQCsample") { :
the condition has length > 1 and only the first element will be used
> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ChIPQC_1.6.1               DiffBind_1.16.3            locfit_1.5-9.1             GenomicAlignments_1.6.3
[5] Rsamtools_1.22.0           Biostrings_2.38.4          XVector_0.10.0             limma_3.26.8
[9] SummarizedExperiment_1.0.2 Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3
[13] IRanges_2.4.8              S4Vectors_0.8.11           BiocGenerics_0.16.1        ggplot2_2.1.0
[17] RSQLite_1.0.0              DBI_0.3.1 

ChIPQC • 1.0k views
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Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 19 days ago
CRUK, Cambridge, UK

Hi Meeta,

We need some more information to figure out what is happening. Is "samples" a samplesheet, a DiffBind (DBA) object, or a SampleList? Could you share more of your script and/or data (peak files etc.), perhaps send me a link at my email:

rory.stark@cruk.cam.ac.uk

Regards-

Rory

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Entering edit mode

Hi Rory,

Many thanks for your quick response, I have emailed you additional information please let me know if there is anything else I can provide!

Meeta

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Entering edit mode

Hi Rory,

It will be better if you share the solution for Meeta problem. I am also facing the same problem. I am giving the following command.

qc_test<- ChIPQC(samples,annotaiton="hg19") where samples is a csv sample sheet.

Error in sample 1: could not find function "seqlevels<-"
Warning messages:
1: In if (class(sample) != "ChIPQCsample") { ... :
the condition has length > 1 and only the first element will be used

sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2 GenomicFeatures_1.20.6                  AnnotationDbi_1.30.1                    Biobase_2.28.0                          ChIPQC_1.4.4
[6] ggplot2_2.1.0                           DiffBind_1.14.6                         RSQLite_1.0.0                           DBI_0.4-1                               locfit_1.5-9.1
[11] GenomicAlignments_1.4.2                 Rsamtools_1.20.5                        Biostrings_2.36.4                       XVector_0.8.0                           limma_3.24.15
[16] GenomicRanges_1.20.8                    GenomeInfoDb_1.4.3                      IRanges_2.2.9                           S4Vectors_0.6.6                         BiocGenerics_0.14.0
[21] BiocInstaller_1.18.5

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
1: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'Matrix' is missing or broken
2: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'survival' is missing or broken

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Entering edit mode

hi anil,

I believe there is a fix in ChIPQC release 1.8.2 related to Meeta's issue which may fix what you are seeing.

If this doesnt help could you post some information on what your samplesheet looks like?

I notice a small typo in your command as well but i am unsure if this is the root of the issue.

qc_test<- ChIPQC(samples,annotaiton="hg19")

should be

qc_test<- ChIPQC(samples,annotation="hg19")

best,

tom