Hello All,

I am receiving an error when inputing my data into DiffBind...dba(sampleSheet="TCGA_DiffBind.csv"). 

I have created a sample sheet file as described in the Diffbind tutorial:

  SampleID Tissue  Factor                                                                       bamReads ControlID
3     M026   SKCM H3K4me3 KRai-TCGA-Epigenomics-TCGA-SKCM-M026-R1-P011-C-SC-MGM-t1B8Da9EC3g-T.sorted.bam     M026c
4     M028   SKCM H3K4me3             KRai-TCGA-Epigenomics-TCGA-SKCM-M028-R1-P008-C-NC-CJT-T.sorted.bam     M028c
5     M035   SKCM H3K4me3             KRai-TCGA-Epigenomics-TCGA-SKCM-M035-R1-P010-C-SC-CJT-T.sorted.bam     M035c
6     M137   SKCM H3K4me3             KRai-TCGA-Epigenomics-TCGA-SKCM-M137-R1-P008-C-NC-CJT-T.sorted.bam     M137c
7     M142   SKCM H3K4me3             KRai-TCGA-Epigenomics-TCGA-SKCM-M142-R1-P010-C-SC-CJT-T.sorted.bam     M142c
8     M177   SKCM H3K4me3             KRai-TCGA-Epigenomics-TCGA-SKCM-M177-R1-P008-C-NC-CJT-T.sorted.bam     M177c
                                                                      bamControl
3 KRai-TCGA-Epigenomics-TCGA-SKCM-M026-R1-P011-G-SC-MGM-tF342a17B9g-T.sorted.bam
4             KRai-TCGA-Epigenomics-TCGA-SKCM-M028-R1-P008-G-NC-CJT-T.sorted.bam
5             KRai-TCGA-Epigenomics-TCGA-SKCM-M035-R1-P010-G-SC-CJT-T.sorted.bam
6             KRai-TCGA-Epigenomics-TCGA-SKCM-M137-R1-P008-G-NC-CJT-T.sorted.bam
7             KRai-TCGA-Epigenomics-TCGA-SKCM-M142-R1-P010-G-SC-CJT-T.sorted.bam
8             KRai-TCGA-Epigenomics-TCGA-SKCM-M177-R1-P008-G-NC-CJT-T.sorted.bam
                                                                          Peaks Peakcaller
3 KRai-TCGA-Epigenomics-TCGA-SKCM-M026-R1-P011-C-SC-MGM-t1B8Da9EC3g-T_peaks.bed        bed
4             KRai-TCGA-Epigenomics-TCGA-SKCM-M028-R1-P008-C-NC-CJT-T_peaks.bed        bed
5             KRai-TCGA-Epigenomics-TCGA-SKCM-M035-R1-P010-C-SC-CJT-T_peaks.bed        bed
6             KRai-TCGA-Epigenomics-TCGA-SKCM-M137-R1-P008-C-NC-CJT-T_peaks.bed        bed
7             KRai-TCGA-Epigenomics-TCGA-SKCM-M142-R1-P010-C-SC-CJT-T_peaks.bed        bed
8             KRai-TCGA-Epigenomics-TCGA-SKCM-M177-R1-P008-C-NC-CJT-T_peaks.bed        bed

I subsequently created a cvs file using...write.csv(TCGA_4, "TCGA_DiffBind.csv", row.names = F) and then read the file into DiffBind using...dba(sampleSheet="TCGA_DiffBind.csv") but get the follow error. 

M026 SKCM H3K4me3   NA raw
Error in Summary.factor(c(1L, 112L, 223L, 315L, 326L, 337L, 348L, 359L,  :
  ‘max’ not meaningful for factors

I have also tried writing tables and reimporting them using read.csv etc but did not have any luck. 

Any help would be greatly appreciated!

Thanks very much!

The "Peakcaller" column should be called "PeakCaller" (uppercase C).  Notice in the output that the first row is shown as having peak format "raw", which means it'll look for scores in column 4, which (if your peaks are bed) is the name column.  Try changing the column heading to "PeakCaller".

(Just for the sake of having an actual "answer" as opposed to a comment...)