Hello all,
IMPORTANT:
- sample
NA19095.5.M_120131_5 should be excluded from all analyses. This
sample is one of the 5 replicates, and for this individual we
originally chose another sample (NA19095.2.M_120131_2) to use. Thus,
the set of unique 462 samples (which should be used in most
analyses) doesn't change. However, if you're analyzing replicates in
any way, exclude NA19095.5.M_120131_5.
Some more info: Peter did analysis of sex-specific expression, which
generally shows very nice clustering to female and male samples.
However, 4 samples showed a mixed pattern that is suggestive of
cross-contamination. Three of these have been excluded previously
due to them showing clear signs of contamination in ASE analysis (
NA12399.7.M_120219_1,
NA07000.1.M_120209_2,
HG00237.4.M_120208_1). However, the sample NA19095.5.M_120131_5
behaved slightly abnormally in ASE analysis but was not excluded
based on that, but the sex-specific analysis shows that this sample
needs to be thrown out.
Additionally, there are some QC warnings for samples that will be
kept in the dataset. In the sex-specific transcription analysis the
sample
NA11930.3.M_120202_8 behaved slightly abnormally, and Jonas and Olof
have also listed samples that are slight outliers based on different
statistics.
An updated sample information sheet is in the attachment. The
UseThisSample flag gives you the set of 462 unique samples (and
hasn't changed from the previous file
(GD667_mRNA_SampleInformation_270712.txt). Additionally, the QC_OK
column denotes all the samples that have passed QC, and QC_Info has
information of why a sample failed QC, or QC warnings for QC-passed
samples, and these two columns have been updated with the
information above.
This information can be found in the wiki
(http://sanabre.net/geuvadis/index.php/QC_sample_info), and the
sample information sheets have been uploaded on the ftp site
(/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qc)
best,
Tuuli
--
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen@unige.ch