Hi all,
First to thank you Mark , Henrik for nice tool and also all others
for informative mailing list.
This is my first email so hopefully not so many dummy questions.
I found this thread as it is linked to my first 2 questions:
Month ago I did some basic analysis with 300 chips where your tool
got very handy. And I'm starting again to analyze things ...
(Btw. I found about Aroma on BioC list as I had issue with XPS
package that I couldn’t resolve . I would like to have them both
working so Xps will come on board eventually.)
Now regarding this tread.
1) When I compared HuGene-1_0-st-v1.na30.hg19.probeset._csv. with
the Aroma CDF file there are
33257 PSets in csv while Aroma has 33252 so 4 different. So
maybe the CDF update is needed in Aroma?
I also just saw some more recent update on Affymetrix to “na30.1”
and I see I have used “na30” csv file.
Following seems weird , many ProbeSets have no gene symbol
annotation in “main“ category :
tr <- read.csv ( "HuGene-1_0-st-v1.na30.hg19.transcript.csv" ,
stringsAsFactors =F ,comment.char="#")
sum(tr$gene_assignment=="---" & tr$category=="main") #6711
sum(tr$unigene=="---" & tr$category=="main") #7376
sum(tr$swissprot=="---" & tr$category=="main") # 8021
Affy 33257 Probesets are classified as:
TYPE TOTAL
control->affx 57
control->bgp->antigenomic 45
main 28829
normgene->exon 1195
normgene->intron 2904
rescue->FLmRNA->unmapped 227
Do you maybe know why are there so many e.g above 6711 without
gene_assignment ?
2) One more related to 1st Q : How to run normalization only on
ProbeSet classified as “main” ? ( Affymetrix csv file says this
class has 28829
Psets in main class) Idea is of course to minimize
normalization bias of non-main class Psets.
3) Few questions regarding Quality checks and basic data
manipulations in Aroma:
I would like to give meaningful labels to the Arrays in the e.g.
box-plots (instead of CEL file names, as said i have 300) .
How can I do that?
Also how can I sort them ?
I ask this silly questions because Using R commands like str()
doesn’t show me the
object fields etc. so I can’t use standard R matrix commands,
also help (“some Aroma command” ) doesn’t show enough information.
Sometimes it gives empty help page.
I could not find pdf manual in Aroma installed libraries nor in
the Google group. I see only html file showing me all the functions &
classes.
Is there easier way to look for functions than main html pages ?
Code of functions are not visible by just typing func.name() , I
guess I can always get source code and search but there is likely easy
way to do it.
It is visible that Aroma uses different classes than
BioConductor. I assume there is a good reason for that, but maybe you
can give some link with explanation?
Oh and thank you for putting clean instructions for basic
preprocessing steps to get Expression matrix out for further
analysis.
One example of my attempt to searching things :
cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
print(cs)
str(cs)
#Classes 'AffymetrixCelSet', 'AffymetrixFileSet',
'AromaPlatformInterface', 'AromaMicroarrayDataSet',
'GenericDataFileSet', 'FullNameInterface', 'Object' atomic [1:1] NA
….
?classname put me on some track.
So I looked a bit and I saw GenericDataFileSet class provides
function
getFullNames() and it does give me the my CEL filenames (btw.
help on ?getFullNames gives me no help .)
setNames() point to basic library… but before going deeper and
making some mess I hope you
can give me answer on above questions or some links ?
4) Last one , regarding QC issue with plotting … SO when doing Array
(pseudo) image plots my RGui in windows complains e.g.:
If I do: cf <- getFile (cs, 1)
plotImage(cf, transform=list(log2), palette=rainbow
(256))
#Loading required package: EBImage
#Loading required package: abind
….
I get “Runtime error!” message from Visual C++ and I have to
click 2 times “ok” and then I get the picture…
Here is the link to the error msg::
http://www.4shared.com/file/209798878/f5a3f82e/Aromaplotimageerror.html
SO you can imagine I’m not enthusiastic of clicking twice for 300
arrays and then again for several type of plots.
Any idea where is the issue ? (I guess something with EBImage
dependency make issue )
Below is my session info .
Hope you can help .
Best regards,
Branko
--------------------------
Branislav Misovic,
Department of Toxicogenetics
Leiden University Medical Center
PO.box 9600, Building2,Room:T3-11
2300 RC Leiden
The Netherlands
Phone: +31 71 526 9636
Mob: 0653135855
E-mail: [email protected]
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods
base
other attached packages:
[1] abind_1.1-0 aroma.affymetrix_1.3.4
aroma.apd_0.1.7
[4] affxparser_1.18.0 R.huge_0.2.0
aroma.core_1.3.4
[7] aroma.light_1.15.1 matrixStats_0.1.8
R.rsp_0.3.6
[10] R.filesets_0.6.5 digest_0.4.1
R.cache_0.2.0
[13] R.utils_1.2.4 R.oo_1.6.6
EBImage_3.2.0
[16] R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] tools_2.10.0
--------------------------
Branislav Misovic,
Department of Toxicogenetics
Leiden University Medical Center
PO.box 9600, Building2,Room:T3-11
2300 RC Leiden
The Netherlands
Phone: +31 71 526 9636
Mob: 0653135855
E-mail: [email protected]
--
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