FAQs - Frequently Asked Questions
Data analysis
Q. What do the columns in the files that I have received mean?
A. This is described by the help file that was supplied with your experimental data.
For more information: Services » Analysis » Downloads » FC004 help file
For more information: Services » Analysis » Downloads » FL002 help file
Q. We have noticed that a couple of genes that we are particularly interested in do not appear in the results files. Could you please explain why?
A. This could be due to one (or more) of the following reasons:
1. The genes are not present in the library that was used to print this microarray format (perhaps true for cDNA arrays)
2. The pin failed to print these probes (rare)
3. The gene you refer to is either not expressed or only weakly expressed (most likely)
For more information: Services » Core Drosophila Microarrays
For more information: Protocols » Robotic Spotting
For more information: Services » Analysis » Downloads
Q. Why are some genes reported more than once?
A. In some cases, this is because some genes have multiple transcripts and we have a probe that is specific for each. In most cases, it will be because this is a control spot and we have printed this multiple times across the microarray.
For more information: Services » Core Drosophila Microarrays
For more information: Services » Analysis » Downloads
Q. Why do the raw and normalised data files have a different number of rows?
A. The is because we remove the not printed, empty, PCR failures, etc., spots from the normalised data file. These spots are, however, included in the raw data files because these files are provided for you those who wish to do so to perform their own normalisation.
For more information: Services » Analysis » Downloads » FC004 help file
For more information: Services » Analysis » Downloads » FL002 help file
Q. What do the positive and negative log ratios mean?
A. A positive log ratio means that the Cy5-labelled sample was over-expressed, compared to the Cy3-labelled sample. A negative value indicates that the Cy5-labelled sample was under-expressed, compared to the Cy3-labelled sample. The sample pairings that were used to perform your microarray hybridisations are described in the Pnnnnn_info.txt file, where nnnnn is your project number. This file records the dye swap status for each hybridisation. Since the swap status is taken into account during the analysis, all hybridisations can be treated as if no dye swap had been performed. This means that the over-expressed sample is the one that was labelled with Cy5 and the under-expressed sample is the one that was labelled with Cy3, when the dye swap status is zero.
For more information: Services » Analysis » Downloads » FC004 help file
For more information: Services » Analysis » Downloads » FL002 help file
For more information: Services » Analysis
