Question

Error involving ChIPQCreport

0

Entering edit mode

Roger • 0

@roger-12673

Last seen 3.2 years ago

Netherlands

Hi,

I have only recently come across ChIPQC, but I find it incredibly useful, especially in combination with Diffbind. Unfortunately, I can only use some its functionalities at the moment, as I keep encountering an error when I run the ChIPQCreport function:

sam = ChIPQC("DBsheet_SzabiChipSeq1.csv")
ChIPQCreport(sam)
Error in `*tmp*`[2] : object of type 'environment' is not subsettable

Calling traceback() reveals that the error occurs with plotRap(), which I next confirmed by attempting to run it separately, only to get the same error.

6: plotRap(object, facetBy = facetBy, addMetaData = addMetaData)
5: plotRap(object, facetBy = facetBy, addMetaData = addMetaData)
4: grid.draw(plot)
3: ggsave(plotRap(object, facetBy = facetBy, addMetaData = addMetaData),
       filename = file.path(reportFolder, "Rap.png"))
2: ChIPQCreport(sam)
1: ChIPQCreport(sam)

Interestingly, when I run either the function or the report with a single sample (i.e. with QCsample), everything works fine. Just to make sure that there are no conflicting samples, I tried with every one of them individually, and they all succeeded. The same happened when I took an entirely different dataset and I repeated my previous steps: the report of the experiment failed, but individual samples were ok.

Am I doing anything wrong? This is my sample sheet:

SampleID	Tissue	Condition	bamReads	Replicates	Peaks	PeakCaller
MOLM1	MOLM1	MOLM1	MOLM1_161128_SN583_0220_AHGGYLADXY.bam	1	MOLM1_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak	narrow
MUTZ3	MUTZ3	MUTZ3	MUTZ3_161128_SN583_0220_AHGGYLADXY.bam	1	MUTZ3_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak	narrow
CD34negCD15neg	MUTZ3	CD34negCD15neg	MUTZ3_CD34neg_CD15neg_161128_SN583_0220_AHGGYLADXY.bam	1	MUTZ3_CD34neg_CD15neg_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak	narrow
CD34negCD15pos	MUTZ3	CD34negCD15pos	MUTZ3_CD34neg_CD15pos_161128_SN583_0220_AHGGYLADXY.bam	1	MUTZ3_CD34neg_CD15pos_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak	narrow
Bulk	MUTZ3	Bulk	MUTZ3_CD34neg_CD34pos_CD15neg_CD15pos_bulk_161128_SN583_0220_AHGGYLADXY.bam	1	MUTZ3_CD34neg_CD34pos_CD15neg_CD15pos_bulk_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak	narrow
CD34posCD15neg	MUTZ3	CD34posCD15neg	MUTZ3_CD34pos_CD15neg_161128_SN583_0220_AHGGYLADXY.bam	1	MUTZ3_CD34pos_CD15neg_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak	narrow

I am aware that we have no replicates, but that is something we are currently working on.

Thanks in advance,

Roger

ChIPQC • 1.8k views

ADD COMMENT • link updated 7.7 years ago by Thomas Carroll ▴ 420 • written 7.7 years ago by Roger • 0

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Thomas Carroll ▴ 420

@thomas-carroll-7019

Last seen 2.1 years ago

United States/New York/The Rockefeller …

hi Roger, I am not quite sure what the problem is here. I think, as you suggest it may be due to have one replicate. Could you try ChIPQCreport(sam,colourBy = NULL). This should solve the issue but if not would you mind sharing the ChIPQCexperiment object "sam" with me offlist at my email tc.infomatics@gmail.com ? If it is a problem useful to others we can post back our solution here. Thanks tom On Thu, Mar 23, 2017 at 2:53 PM, roger.mulet [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User roger.mulet <https: support.bioconductor.org="" u="" 12673=""/> wrote Question: > Error involving ChIPQCreport <https: support.bioconductor.org="" p="" 94150=""/>: > > Hi, > > I have only recently come across ChIPQC, but I find it incredibly useful, > especially in combination with Diffbind. Unfortunately, I keep encountering > an error when I run the ChIPQCreport function: > > sam = ChIPQC("DBsheet_SzabiChipSeq1.csv") > > ChIPQCreport(sam) > > Error in `*tmp*`[2] : object of type 'environment' is not subsettable > > Calling traceback() reveals that the error occurs with plotRap(), which I > next confirmed by attempting to run it separately, only to get the same > error. > > 6: plotRap(object, facetBy = facetBy, addMetaData = addMetaData) > 5: plotRap(object, facetBy = facetBy, addMetaData = addMetaData) > 4: grid.draw(plot) > 3: ggsave(plotRap(object, facetBy = facetBy, addMetaData = addMetaData), > filename = file.path(reportFolder, "Rap.png")) > 2: ChIPQCreport(sam) > 1: ChIPQCreport(sam) > > Interestingly, when I run either the function or the report with a single > sample (i.e. with QCsample), everything works fine. Just to make sure that > there are no conflicting samples, I tried with every one of them > individually, and they all succeeded. The same happened when I took an > entirely different dataset and I repeated my previous steps: the report of > the experiment failed, but individual samples were ok. > > Am I doing anything wrong? This is my sample sheet: > SampleID Tissue Condition bamReads Replicates Peaks PeakCaller > MOLM1 MOLM1 MOLM1 MOLM1_161128_SN583_0220_AHGGYLADXY.bam 1 > MOLM1_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak narrow > MUTZ3 MUTZ3 MUTZ3 MUTZ3_161128_SN583_0220_AHGGYLADXY.bam 1 > MUTZ3_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak narrow > CD34negCD15neg MUTZ3 CD34negCD15neg MUTZ3_CD34neg_CD15neg_161128_ > SN583_0220_AHGGYLADXY.bam 1 MUTZ3_CD34neg_CD15neg_161128_ > SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak narrow > CD34negCD15pos MUTZ3 CD34negCD15pos MUTZ3_CD34neg_CD15pos_161128_ > SN583_0220_AHGGYLADXY.bam 1 MUTZ3_CD34neg_CD15pos_161128_ > SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak narrow > Bulk MUTZ3 Bulk MUTZ3_CD34neg_CD34pos_CD15neg_CD15pos_bulk_161128_SN583_ > 0220_AHGGYLADXY.bam 1 MUTZ3_CD34neg_CD34pos_CD15neg_ > CD15pos_bulk_161128_SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak narrow > CD34posCD15neg MUTZ3 CD34posCD15neg MUTZ3_CD34pos_CD15neg_161128_ > SN583_0220_AHGGYLADXY.bam 1 MUTZ3_CD34pos_CD15neg_161128_ > SN583_0220_AHGGYLADXY_peaks_filtered.narrowPeak narrow > > I am aware that we have no replicates, but that is something we are > currently working on. > > Thanks in advance, > > Roger > > ------------------------------ > > Post tags: ChIPQC > > You may reply via email or visit Error involving ChIPQCreport >

ADD COMMENT • link 7.7 years ago Thomas Carroll ▴ 420

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Roger • 0

@roger-12673

Last seen 3.2 years ago

Netherlands

Hi Thomas,

Thanks for your quickly reply and apologies for my delay - I have been away from the office for a few days. I tried your suggestion, but unfortunately it did not work. I have just sent you an RData file containing the ChIPQCexperiment object I created (sam). I hope I am not doing anything terribly silly!

Cheers,

Roger

ADD COMMENT • link 7.7 years ago Roger • 0

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hi Roger, Sorry for the delay. There was some change in the ggplot2 internal structure which was causing some plots to fail. I have made the changes to fix this which will be available in ChIPQC 1.10.3. This should build tonight and be available to you in the morning or you can grab from read only svn now and build. Let me know if you have an issues. best, tom On Tue, Mar 28, 2017 at 1:40 PM, Roger [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Roger <https: support.bioconductor.org="" u="" 12673=""/> wrote Answer: > Error involving ChIPQCreport > <https: support.bioconductor.org="" p="" 94150="" #94262="">: > > Hi Thomas, > > Thanks for your quickly reply and apologies for my delay - I have been > away from the office for a few days. I tried your suggestion, but > unfortunately it did not work. I have just sent you an RData file > containing the ChIPQCexperiment object I created (sam). I hope I am not > doing anything terribly silly! > > Cheers, > > Roger > > ------------------------------ > > Post tags: ChIPQC > > You may reply via email or visit https://support.bioconductor. > org/p/94150/#94262 >

ADD REPLY • link 7.7 years ago Thomas Carroll ▴ 420

score 2 · Accepted Answer · 2017-04-03

2

Entering edit mode

Thomas Carroll ▴ 420

@thomas-carroll-7019

Last seen 2.1 years ago

United States/New York/The Rockefeller …

hi Roger,

Sorry for the delay.

There was some change in the ggplot2 internal structure which was causing some plots to fail. I have made the changes to fix this which will be available in ChIPQC 1.10.3. This should build tonight and be available to you in the morning or you can grab from read only svn now and build.

Let me know if you have an issues.

best,

tom

ADD COMMENT • link 7.7 years ago Thomas Carroll ▴ 420

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Entering edit mode

Hi Tim,

As I told you via email, the issue is fixed on ChIPQC 1.10.3 and now the report is successfully generated. Thanks!

However, in case anyone reading this stumbles upon the same, I would like to report an error uploading the ChIPQC experiment with R version 3.2 and Bioconductor 3.2. The error was gone as soon as I upgraded to R 3.3 (with both Bioconductor 3.3 and 3.4). Maybe it's just me, but I leave the warning here just in case.

ADD REPLY • link 7.7 years ago Roger • 0