Dear Group,
I have been experiencing problems when I try to
process SMD derived .xls files (Raw data). These are
not exactly .XLS files but simply tab delim files.
I am using Limma to normalize the bunch of files.
here are the steps:
>mfiles = list.files(pattern='.xls')
>mdata = read.maimages(mfiles,source='smd')
>mgal = 'my_gal_file'
>layout = getLayout2(mgal)
> layout
$ngrid.r
[1] 12
$ngrid.c
[1] 4
$nspot.r
[1] 30
$nspot.c
[1] 30
attr(,"class")
[1] "PrintLayout"
> ma
=normalizeWithinArrays(mdata,layout,,method='printtiploess',bc.method=
'none')
Error in switch(method, loess = { : printer layout
information does not match M row dimension
Here, I am normalizing without background correction
and thus I am taking mdata object directly to
'normalizeWithinArrays' function.
I looked into the GAL file obtained from SMD.
There are some rows, that are completly empty:
5 27 30 EMPTY EMPTY
5 28 30 EMPTY EMPTY
5 29 30 EMPTY EMPTY
5 30 30 EMPTY EMPTY
Because of these errors, normalizeWithinArrays is
unable to match the spot dimensions and layout file.
I tried to remove these EMPTY EMPTY spots from GAL
file. However, the header information does not match
with adjusted rows after removing EMPTY files:
ATF 1.0
53 5
"Type=GenePix ArrayList V1.0"
"BlockCount=48"
"BlockType=0"
"URL=
http://source.stanford.edu/cgi-bin/source/sourceSearch"
"Block1= 400, 400, 100, 30, 146, 30, 146"
"Block2= 4896, 400, 100, 30, 146, 30, 146"
"Block3= 9392, 400, 100, 30, 146, 30, 146"
"Block4= 13888, 400, 100, 30, 146, 30, 146"
"Block5= 400, 4896, 100, 30, 146, 30, 146"
.....
"Block48=................................"
Thus, although the number of spot information in GAL
file is correct it does not match the header and thus
leads to this error: This is what my guess is.
Also this is what 'Gordon Smith'(See Ref) wrote to
another user some time back for same error.
My question to Limma developers or to any other users
who could overcome this problem is:
1. How can I correct the header BLOCK information of
GAL file for adjusted rows where I find there is no
spot information. simply, how can I make some
adjustments to GAL file and then try to rectify the
situation. Is this possible at all. If not what are
the alternatives.
2. In a nut-shell, how to escape this ':printer layout
information does not match M row...'.
Ref:
https://stat.ethz.ch/pipermail/bioconductor/2005-October/010482.html
Thank you very much in advance.
regards
Sri
