DiffBind DEseq
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浩然 • 0
@-25182
Last seen 4 months ago
Beijing

hi,I run the code successfully:


yap <- dba.count(yap)
yap <- dba.contrast(yap,categories=DBA_CONDITION,minMembers=2)
yap
4 Samples, 31676 sites in matrix:
    ID Condition Treatment Replicate Caller Intervals FRiP
1  IP1        IP        IP         1 counts     31676 0.53
2  IP2        IP        IP         2 counts     31676 0.56
3 IgG1       IgG       IgG         1 counts     31676 0.46
4 IgG2       IgG       IgG         2 counts     31676 0.46

but when I uesd the'dba.analyze',it shows that:

yap <- dba.analyze(yap)
converting counts to integer mode
Error in .local(object, ...) : 
  all genes have equal values for all samples. will not be able to perform differential analysis
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  all genes have equal values for all samples. will not be able to perform differential analysis

and why when i completed the 'dba.contrast', it shows the same 'Intervals'. thank you!!!

DiffBind • 340 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK

I notice that the two IgGs have the same FRiP, are you using two different sets of reads?

You can retrieve the read counts and check if they are different:

yap <- dba.count(yap, peaks=NULL, score=DBA_SCORE_READS)
counts <- dba.peakset(yeap, bRetrieve=TRUE)

Usually when we see this error, either the same bam file is being used for multiple samples, or there are large numbers of control reads which are being subtracted leaving all the counts at 0. (Control reads are subtracted by default if there is no greylist).

If you are subtracting control reads:

yap <- dba.count(yap, peaks=NULL, score=DBA_SCORE_READS_MINUS)
counts <- dba.peakset(yeap, bRetrieve=TRUE)
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thank you, Rory! The same bam file is being used for the multiple samples.

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Are you trying to cheat your way around a lack of replicates?

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yes,I am trying other methods.

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If you have no replicates, no serious software will work. Lying to the software you are using yields garbage.

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The seq file I used was downloading from GEO,unfortunately there is not replicates!

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sorry, I have another trouble.

sampleDba <- dba(sampleSheet = samples)
IP1   IP IP 1 narrow
IP2   IP IP 2 narrow
Error in cbind(pv$class, clascol) :
  number of rows of matrices must match (see arg 2)

And when I use the data that last time I used also return this erro. Thank you !

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