Dear all, This is the sample sheet, I am using.

"SampleID","Tissue","Factor","Condition","Treatment","Replicate","bamReads","Peaks","PeakCaller" "18-133-0011","MCF7","HSF1","MCFNHSchangedhs1","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0012","MCF7","HSF1","MCFNHSchangedhs2","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincchangedHSF1peaksfiltered2sorted.bed","raw" "18-133-0013","MCF7","HSF1","MCFNHSunchangedhs1","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincunchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0014","MCF7","HSF1","MCFNHSunchangedhs2","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincunchangedHSF1peaksfiltered2sorted.bed","raw" "18-133-0015","MCF7","HSF1","MCFNHSchangedas1","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0016","MCF7","HSF1","MCFNHSchangedas2","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0017","MCF7","HSF1","MCFNHSunchangedas1","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincunchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0018","MCF7","HSF1","MCFNHSunchangedas2","untreated",1,"s18133001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincunchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0021","MCF7","HSF1","MCFHSchanged1","heatshock",1,"s18133002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0022","MCF7","HSF1","MCFHSchanged2","heatshock",1,"s18133002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincchangedHSF1peaksfiltered2sorted.bed","raw" "18-133-0023","MCF7","HSF1","MCFHSunchanged1","heatshock",1,"s18133002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincunchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0024","MCF7","HSF1","MCFHSunchanged2","heatshock",1,"s18133002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001002NHSHSwrtHSF1allincunchangedHSF1peaksfiltered2sorted.bed","raw" "18-133-0031","MCF7","HSF1","MCFASchanged1","arsenic",1,"s18133003dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0032","MCF7","HSF1","MCFASchanged2","arsenic",1,"s18133003dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincchangedHSF1peaksfiltered2sorted.bed","raw" "18-133-0033","MCF7","HSF1","MCFASunchanged1","arsenic",1,"s18133003dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincunchangedHSF1peaksfiltered1sorted.bed","raw" "18-133-0034","MCF7","HSF1","MCFASunchanged2","arsenic",1,"s18133003dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18133001003NHSAswrtHSF1allincunchangedHSF1peaksfiltered2sorted.bed","raw" "18-093-0011","MCF7","HSF1","MCFNHSchangedhs1","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincchangedpeaksfiltered1sorted.bed","raw" "18-093-0012","MCF7","HSF1","MCFNHSchangedhs2","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincchangedpeaksfiltered2sorted.bed","raw" "18-093-0013","MCF7","HSF1","MCFNHSunchangedhs1","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincunchangedpeaksfiltered1sorted.bed","raw" "18-093-0014","MCF7","HSF1","MCFNHSunchangedhs2","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincunchangedpeaksfiltered2sorted.bed","raw" "18-093-0015","MCF7","HSF1","MCFNHSchangedas1","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincchangedpeaksfiltered1sorted.bed","raw" "18-093-0016","MCF7","HSF1","MCFNHSchangedas2","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincchangedpeaksfiltered2sorted.bed","raw" "18-093-0017","MCF7","HSF1","MCFNHSunchangedas1","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincunchangedpeaksfiltered1sorted.bed","raw" "18-093-0018","MCF7","HSF1","MCFNHSunchangedas2","untreated",2,"s18093001dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincunchangedpeaksfiltered2sorted.bed","raw" "18-093-0021","MCF7","HSF1","MCFHSchanged1","heatshock",2,"s18093002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincchangedpeaksfiltered1sorted.bed","raw" "18-093-0022","MCF7","HSF1","MCFHSchanged2","heatshock",2,"s18093002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincchangedpeaksfiltered2sorted.bed","raw" "18-093-0023","MCF7","HSF1","MCFHSunchanged1","heatshock",2,"s18093002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincunchangedpeaksfiltered1sorted.bed","raw" "18-093-0024","MCF7","HSF1","MCFHSunchanged2","heatshock",2,"s18093002dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001002NHSHSwrtHSF1allincunchangedpeaksfiltered2sorted.bed","raw" "18-088-0061","MCF7","HSF1","MCFASchanged1","arsenic",2,"18-088-006dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincchangedpeaksfiltered1sorted.bed","raw" "18-088-0062","MCF7","HSF1","MCFASchanged2","arsenic",2,"18-088-006dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincchangedpeaksfiltered2sorted.bed","raw" "18-088-0063","MCF7","HSF1","MCFASunchanged1","arsenic",2,"18-088-006dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincunchangedpeaksfiltered1sorted.bed","raw" "18-088-0064","MCF7","HSF1","MCFASunchanged2","arsenic",2,"18-088-006dedupmarked.bam","/lowerbay/home/bony.dekumar/ForBony/MCF7/filteredlist/s18093001006NHSAswrtHSF1allincunchangedpeaksfiltered2sorted.bed","raw

But, in my PCA plot and Correlation plots, I am seeing only 6 samples. Please let me know what is going wrong here? why I am not seeing other samples? is there any limitation in the number of samples that can be plotted on a PCA plot? Thanks

It would help to see the code you are using.

One possibility is that if you are plotting the results of a contrast (after dba.analyze()), then by default only the samples included in the contrast are plotted. You can, optionally, show other samples as well.

For dba.plotHeatmap(), you can set the mask parameter to say what samples to include; to include all of them, use mask=myDBA$masks$All. The help page for dba.plotHeatmap() has an example of including samples other than those in the contrast. You can also set the mask parameter for dba.plotPCA() to compute that plot the PCA including samples not in the contrast sample groups.