The format expected is essentially the output of a spreadsheet file in ASCII or plain text with the values delimited by tabs, commas, or spaces. If your data are in Excel or a similar spreadsheet program, they should be saved as text files and delimited by tabs, commas, or spaces. Make sure that your labels (gene names) do not include whatever you choose.
Comments can be inserted anywhere in the text as long as the comment lines are prefixed by a '#' because the underlying R code will ignore command lines beginning with #. Column headings must be removed unless they are preficed by a # sign or specifically excluded by identifying which is data start row. Do note that having the # sign in the middle of a line without prefixing the line with a # will result in errors. For example, please ensure that none of the gene names (in the label column) have a # in them.
Missing values are coded as 'NA' (not 'na' - case matters) and values below background are coded as zero ("0")
There must be at least one label column. And columns for the same condition must be contiguous. Examples are given below for each analysis type.
For this type of analysis, where the first condition is a control, and second condition is an experimental, columns should be in this order:
Label, ControlReplicate1, ControlReplicate2, ExperimentalReplicate1, ExperimentalReplicate2
Of course, you can have more than two control or experimental replicates, but they must be contiguous. You cannot have (for example) control columns, then experimental columns, the control columns again.
Here's an example file:
# here's a comment
# and another, and the line below is also a comment which is OK to insert
# Label ContColumn1 ContColumn2 ExpColumn1 ExpColumn2
# the real data starts just after this line
GH01040 0.81888287 0.98072154 1.16866872 1.38928931
GH01059 0.87158715 0.9766095 1.05333957 1.18938903
# comments can be interspersed as long as the line begins with a '#'
GH01066 0.8881064 0.45129639 0.79107254 0.90903492
GH01085 0.53412245 0.84194019 0.95338764 1.22393455
For paired data, you must upload raw measurements of two conditions with an equal number of replicates. Please see the Pairs Help Section for more details of when and why a Paired analysis is appropriate.
With raw measurements, columns should be in the following order:
Label, Cond1Repl1, Cond1Repl2, Cond2Repl1, Cond2Repl2
This means that Cond1Repl1 will be paired with Cond2Repl1, and similarly Cond1Repl2 will be paired with Cond2Repl2. Of course, you can have more than two columns per condition, but the number of columns in each condition must be equal. The Unpaired two conditions data example file from above works as an example for this type of data.
For this type of data, the columns for each condition should be contiguous. For example with three conditions having two replicates each, columns should be in the following order:
Label, Cond1Repl1, Cond1Repl2, Cond2Repl1, Cond2Repl2, Cond3Repl1, Cond3Repl2
Again, you could have more than three conditions or more than two replicates each, but columns from the same condition need to be next to one another. Here is an example file:
# here's a comment
# and another, and the line below is also a comment which is OK to insert
# Label Cond1Column1 Cond1Column2 Cond2Column1 Cond2Column2 Cond3Column1 Cond3Column2
# the real data starts just after this line
GH01040 0.81888287 0.98072154 1.16866872 1.38928931 1.78923471 1.65654518
GH01059 0.87158715 0.9766095 1.05333957 1.18938903 1.54621312 0.99854211
# comments can be interspersed as long as the line begins with a '#'
GH01066 0.8881064 0.45129639 0.79107254 0.90903492 1.46541311 1.64659878
GH01085 0.53412245 0.84194019 0.95338764 1.22393455 0.89154451 0.87973211